Summary: zinc-finger binding domain of transposase IS66

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Wikipedia: Helix-turn-helix
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Helix-turn-helix Edit Wikipedia article

The Î» repressor of bacteriophage lambda employs a helix-turn-helix (left; green) to bind DNA (right; blue and red).

In proteins, the helix-turn-helix (HTH) is a major structural motif capable of binding DNA. It is composed of two Î± helices joined by a short strand of amino acids and is found in many proteins that regulate gene expression. It should not be confused with the helix-loop-helix domain.^[1]

[edit] Discovery

The discovery of the helix-turn-helix motif was based on similarities between several genes encoding transcription regulatory proteins from bacteriophage lambda and Escherichia coli: Cro, CAP, and Î» repressor, which were found to share a common 20-25 amino acid sequence that facilitates DNA recognition.^[2]^[3]^[4]^[5]

[edit] Function

The helix-turn-helix motif is a DNA-binding motif. The recognition and binding to DNA by helix-turn-helix proteins is done by the two Î± helices, one occupying the N-terminal end of the motif, the other at the C-terminus. In most cases, such as in the Cro repressor, the second helix contributes most to DNA recognition, and hence it is often called the "recognition helix". It binds to the major groove of DNA through a series of hydrogen bonds and various Van der Waals interactions with exposed bases. The other Î± helix stabilizes the interaction between protein and DNA, but does not play a particularly strong role in its recognition..^[2] The recognition helix and its preceding helix always have the same relative orientation.^[6]

[edit] Classification of helix-turn-helix motifs

Several attempts have been made to classify the helix-turn-helix motifs based on their structure and the spatial arrangement of their helices^[6]^[7]^[8] Some of the main types are described below.

[edit] Tri-helical

The tri-helical helix-turn-helix motif is the simplest helix-turn-helix motif. It consists only of the three main helices. An example of this motif is found in the Transcriptional activator Myb.^[9]

[edit] Tetra-helical

The tetra-helical helix-turn-helix motif has an additional C-terminal helix compared to the tri-helical motifs. These include the LuxR-type DNA-binding HTH domain found in bacterial transcription factors and the helix-turn-helix motif found in the TetR repressors.^[10] Multihelical versions with additional helices also occur.^[11]

[edit] Winged helix-turn-helix

The winged helix-turn-helix (wHTH) motif is formed by a 3-helical bundle and a 3- or 4-strand beta-sheet (wing). The topology of helices and strands in the wHTH motifs may vary. In the transcription factor ETS wHTH folds into a helix-turn-helix motif on a four-stranded anti-parallel beta-sheet scaffold arranged in the order Î±1-Î²1-Î²2-Î±2-Î±3-Î²3-Î²4 where the third helix is the DNA recognition helix.^[12]^[13]

[edit] Other modified helix-turn-helix motifs

Other derivatives of the helix-turn-helix motif include the DNA-binding domain found in MarR, a regulator of multiple antibiotic resistance, which forms a winged helix-turn-helix with an additional C-terminal alpha helix.^[14]^[8]

[edit] See also

[edit] References

^ Brennan RG, Matthews BW (1989). "The helix-turn-helix DNA binding motif.". J Biol Chem 264 (4): 1903â6. PMID 2644244.
^ ^a ^b Matthews BW, Ohlendorf DH, Anderson WF, Takeda Y (1982). "Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor.". Proc Natl Acad Sci U S A 79 (5): 1428â32. doi:10.1073/pnas.79.5.1428. PMC 345986. PMID 6951187. //www.ncbi.nlm.nih.gov/pmc/articles/PMC345986/.
^ Anderson WF, Ohlendorf DH, Takeda Y, Matthews BW (1981). "Structure of the cro repressor from bacteriophage lambda and its interaction with DNA.". Nature 290 (5809): 754â8. doi:10.1038/290754a0. PMID 6452580.
^ McKay DB, Steitz TA (1981). "Structure of catabolite gene activator protein at 2.9 A resolution suggests binding to left-handed B-DNA.". Nature 290 (5809): 744â9. doi:10.1038/290744a0. PMID 6261152.
^ Pabo CO, Lewis M (1982). "The operator-binding domain of lambda repressor: structure and DNA recognition.". Nature 298 (5873): 443â7. doi:10.1038/298443a0. PMID 7088190.
^ ^a ^b Wintjens R, Rooman M (1996). "Structural classification of HTH DNA-binding domains and protein-DNA interaction modes.". J Mol Biol 262 (2): 294â313. doi:10.1006/jmbi.1996.0514. PMID 8831795. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=8831795.
^ Suzuki M, Brenner SE (1995). "Classification of multi-helical DNA-binding domains and application to predict the DBD structures of sigma factor, LysR, OmpR/PhoB, CENP-B, Rapl, and Xy1S/Ada/AraC.". FEBS Lett 372 (2-3): 215â21. doi:10.1016/0014-5793(95)00988-L. PMID 7556672.
^ ^a ^b Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM (2005). "The many faces of the helix-turn-helix domain: transcription regulation and beyond.". FEMS Microbiol Rev 29 (2): 231â62. doi:10.1016/j.femsre.2004.12.008. PMID 15808743. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=15808743.
^ Ogata K, Hojo H, Aimoto S, Nakai T, Nakamura H, Sarai A et al. (1992). "Solution structure of a DNA-binding unit of Myb: a helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core.". Proc Natl Acad Sci U S A 89 (14): 6428â32. doi:10.1073/pnas.89.14.6428. PMC 49514. PMID 1631139. //www.ncbi.nlm.nih.gov/pmc/articles/PMC49514/.
^ Hinrichs W, Kisker C, DÃ¼vel M, MÃ¼ller A, Tovar K, Hillen W et al. (1994). "Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance.". Science 264 (5157): 418â20. doi:10.1126/science.8153629. PMID 8153629.
^ Iwahara J, Clubb RT (1999). "Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID).". EMBO J 18 (21): 6084â94. doi:10.1093/emboj/18.21.6084. PMC 1171673. PMID 10545119. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1171673/.
^ Donaldson LW, Petersen JM, Graves BJ, McIntosh LP (1996). "Solution structure of the ETS domain from murine Ets-1: a winged helix-turn-helix DNA binding motif". EMBO J. 15 (1): 125â34. PMC 449924. PMID 8598195. //www.ncbi.nlm.nih.gov/pmc/articles/PMC449924/.
^ Sharrocks AD, Brown AL, Ling Y, Yates PR (1997). "The ETS-domain transcription factor family". Int. J. Biochem. Cell Biol. 29 (12): 1371â87. doi:10.1016/S1357-2725(97)00086-1. PMID 9570133.
^ Alekshun MN, Levy SB, Mealy TR, Seaton BA, Head JF (2001). "The crystal structure of MarR, a regulator of multiple antibiotic resistance, at 2.3 A resolution.". Nat Struct Biol 8 (8): 710â4. doi:10.1038/90429. PMID 11473263. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=11473263.

[edit] Further reading

Struhl K (1989). "Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins.". Trends Biochem Sci 14 (4): 137â40. doi:10.1016/0968-0004(89)90145-X. PMID 2499084. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=2499084.
Gajiwala KS, Burley SK (2000). "Winged helix proteins.". Curr Opin Struct Biol 10 (1): 110â6. PMID 10679470. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=10679470.
Santos CL, Tavares F, Thioulouse J, Normand P (2009). "A phylogenomic analysis of bacterial helix-turn-helix transcription factors.". FEMS Microbiol Rev 33 (2): 411â29. doi:10.1111/j.1574-6976.2008.00154.x. PMID 19076237. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=19076237.
Hoskisson PA, Rigali S (2009). "Chapter 1: Variation in form and function the helix-turn-helix regulators of the GntR superfamily.". Adv Appl Microbiol 69: 1â22. doi:10.1016/S0065-2164(09)69001-8. PMID 19729089. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=19729089.
Brennan RG (1993). "The winged-helix DNA-binding motif: another helix-turn-helix takeoff.". Cell 74 (5): 773â6. doi:10.1016/0092-8674(93)90456-Z. PMID 8374950. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=8374950.
Huffman JL, Brennan RG (2002). "Prokaryotic transcription regulators: more than just the helix-turn-helix motif.". Curr Opin Struct Biol 12 (1): 98â106. PMID 11839496. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=11839496.

[edit] External links

Pfam infoboxes for Helix-turn-helix domains

Bacterial regulatory helix-turn-helix protein, lysR family

Identifiers

Symbol

HTH_1

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

HTH DNA binding domain

Identifiers

Symbol

HTH_10

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Ribonuclease R winged-helix domain

Identifiers

Symbol

HTH_12

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

HTH DNA binding domain

Identifiers

Symbol

HTH_13

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix

Identifiers

Symbol

HTH_3

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Bacterial regulatory protein, arsR family

Identifiers

Symbol

HTH_5

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix domain, rpiR family

Identifiers

Symbol

HTH_6

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix domain of resolvase

Identifiers

Symbol

HTH_7

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Bacterial regulatory protein, Fis family

Identifiers

Symbol

HTH_8

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

RNA polymerase III subunit RPC82 helix-turn-helix domain

Identifiers

Symbol

HTH_9

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Bacterial regulatory helix-turn-helix proteins, AraC family

Identifiers

Symbol

HTH_AraC

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

CodY helix-turn-helix domain

Identifiers

Symbol

HTH_CodY

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

DeoR-like helix-turn-helix domain

Identifiers

Symbol

HTH_DeoR

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

IclR helix-turn-helix domain

Identifiers

Symbol

HTH_IclR

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

M protein trans-acting positive regulator (MGA) HTH domain

Identifiers

Symbol

HTH_Mga

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix domain

Identifiers

Symbol

HTH_OrfB_IS605

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

helix-turn-helix, Psq domain

Identifiers

Symbol

HTH_psq

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Transposase

Identifiers

Symbol

HTH_Tnp_1

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Transposase

Identifiers

Symbol

HTH_Tnp_IS630

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Mu DNA-binding domain

Identifiers

Symbol

HTH_Tnp_Mu_1

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Mu DNA binding, I gamma subdomain

Identifiers

Symbol

HTH_Tnp_Mu_2

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Transposase

Identifiers

Symbol

HTH_Tnp_Tc3_2

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Tc5 transposase DNA-binding domain

Identifiers

Symbol

HTH_Tnp_Tc5

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Sporulation Regulator WhiA C terminal domain

Identifiers

Symbol

HTH_WhiA

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix domain of alkylmercury lyase

Identifiers

Symbol

HTH_15

Pfam

PF12324

Pfam clan

CL0123

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix domain

Identifiers

Symbol

HTH_16

Pfam

PF12645

Pfam clan

CL0123

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix domain

Identifiers

Symbol

HTH_17

Pfam

PF12728

Pfam clan

CL0123

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix domain

Identifiers

Symbol

HTH_18

Pfam

PF12833

Pfam clan

CL0123

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix domain

Identifiers

Symbol

HTH_19

Pfam

PF12844

Pfam clan

CL0123

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Helix-turn-helix domain

Identifiers

Symbol

HTH_20

Pfam

PF12840

Pfam clan

CL0123

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

InsA C-terminal domain

Identifiers

Symbol

HTH_Tnp_IS1

Pfam

PF12759

Pfam clan

CL0123

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

putative Helix-turn-helix domain of transposase IS66

Identifiers

Symbol

HTH_Tnp_IS66

Pfam

PF13005

Pfam clan

CL0123

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

HTH domain

Identifiers

Symbol

HTH_11

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Tc3 transposase

Identifiers

Symbol

HTH_Tnp_Tc3_1

Pfam

PF11427

Pfam clan

CL0123

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

v t e Protein secondary structure

Protein secondary structure	Helices: Î±-helix Â· 3₁₀ helix Â· Ï-helix Â· Î²-helix Â· Polyproline helix Â· Collagen helix Extended: Î²-strand Â· Turn Â· Beta hairpin Â· Beta bulge Â· Î±-strand Supersecondary: Coiled coil Â· Helix-turn-helix Â· EF hand

Amino acids	Helix-favoring: Methionine Â· Alanine Â· Leucine Â· Glutamic acid Â· Glutamine Â· Lysine Extended-favoring: Threonine Â· Isoleucine Â· Valine Â· Phenylalanine Â· Tyrosine Â· Tryptophan Disorder-favoring: Glycine Â· Serine Â· Proline Â· Asparagine Â· Aspartic acid No preference: Cysteine Â· Histidine Â· Arginine

âPrimary structure Tertiary structureâ

Transcription factors and intracellular receptors

(1) Basic domains

(1.1) Basic leucine zipper (bZIP)	Activating transcription factor (AATF, 1, 2, 3, 4, 5, 6, 7) Â· AP-1 (c-Fos, FOSB, FOSL1, FOSL2, JDP2, c-Jun, JUNB, JUND) Â· BACH (1, 2) Â· BATF Â· BLZF1 Â· C/EBP (Î±, Î², Î³, Î´, Îµ, Î¶) Â· CREB (1, 3, L1) Â· CREM Â· DBP Â· DDIT3 Â· GABPA Â· HLF Â· MAF (B, F, G, K) Â· NFE (2, L1, L2, L3) Â· NFIL3 Â· NRL Â· NRF (1, 2, 3) Â· XBP1

(1.2) Basic helix-loop-helix (bHLH)	ATOH1 Â· AhR Â· AHRR Â· ARNT Â· ASCL1 Â· BHLH (2, 9) Â· BMAL (ARNTL, ARNTL2) Â· CLOCK Â· EPAS1 Â· FIGLA Â· HAND (1, 2) Â· HES (5, 6) Â· HEY (1, 2, L) Â· HES1 Â· HIF (1A, 3A) Â· ID (1, 2, 3, 4) Â· LYL1 Â· MESP2 Â· MXD4 Â· MYCL1 Â· MYCN Â· Myogenic regulatory factors (MyoD, Myogenin, MYF5, MYF6) Â· Neurogenins (1, 2, 3) Â· NeuroD (1, 2) Â· NPAS (1, 2, 3) Â· OLIG (1, 2) Â· Pho4 Â· Scleraxis Â· SIM (1, 2) Â· TAL (1, 2) Â· Twist Â· USF1

(1.3) bHLH-ZIP	AP-4 Â· MAX Â· MITF Â· MNT Â· MLX Â· MXI1 Â· Myc Â· SREBP (1, 2)

(1.4) NF-1	NFI (A, B, C, X) Â· SMAD (R-SMAD (1, 2, 3, 5, 9) - I-SMAD (6, 7) - 4)

(1.5) RF-X	RFX (1, 2, 3, 4, 5, 6, ANK)

(1.6) Basic helix-span-helix (bHSH)	AP-2 (Î±, Î², Î³, Î´, Îµ)

(2) Zinc finger DNA-binding domains

(2.1) Nuclear receptor (Cys₄)	subfamily 1 (Thyroid hormone (Î±, Î²), CAR, FXR, LXR (Î±, Î²), PPAR (Î±, Î²/Î´, Î³), PXR, RAR (Î±, Î², Î³), ROR (Î±, Î², Î³), Rev-ErbA (Î±, Î²), VDR) subfamily 2 (COUP-TF (I, II), Ear-2, HNF4 (Î±, Î³), PNR, RXR (Î±, Î², Î³), Testicular receptor (2, 4), TLX) subfamily 3 (Steroid hormone (Androgen, Estrogen (Î±, Î²), Glucocorticoid, Mineralocorticoid, Progesterone), Estrogen related (Î±, Î², Î³)) subfamily 4 NUR (NGFIB, NOR1, NURR1) Â· subfamily 5 (LRH-1, SF1) Â· subfamily 6 (GCNF) Â· subfamily 0 (DAX1, SHP)

(2.2) Other Cys₄	GATA (1, 2, 3, 4, 5, 6) Â· MTA (1, 2, 3) Â· TRPS1

(2.3) Cys₂His₂	General transcription factors (TFIIA, TFIIB, TFIID, TFIIE (1, 2), TFIIF (1, 2), TFIIH (1, 2, 4, 2I, 3A, 3C1, 3C2)) ATBF1 Â· BCL (6, 11A, 11B) Â· CTCF Â· E4F1 Â· EGR (1, 2, 3, 4) Â· ERV3 Â· GFI1 Â· GLI-KrÃ¼ppel family (1, 2, 3, REST, S2, YY1) Â· HIC (1, 2) Â· HIVEP (1, 2, 3) Â· IKZF (1, 2, 3) Â· ILF (2, 3) Â· KLF (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17) Â· MTF1 Â· MYT1 Â· OSR1 Â· PRDM9 Â· SALL (1, 2, 3, 4) Â· SP (1, 2, 4, 7, 8) Â· TSHZ3 Â· WT1 Â· Zbtb7 (7A, 7B) Â· ZBTB (11, 16, 17, 20, 32, 33, 40) Â· zinc finger (3, 7, 9, 10, 19, 22, 24, 33B, 34, 35, 41, 43, 44, 51, 74, 143, 146, 148, 165, 202, 217, 219, 238, 239, 259, 267, 268, 281, 295, 300, 318, 330, 346, 350, 365, 366, 384, 423, 451, 452, 471, 593, 638, 644, 649, 655)

(2.4) Cys₆	HIVEP1

(2.5) Alternating composition	AIRE Â· DIDO1 Â· GRLF1 Â· ING (1, 2, 4) Â· JARID (1A, 1B, 1C, 1D, 2) Â· JMJD1B

(3) Helix-turn-helix domains

(3.1) Homeodomain	ARX Â· CDX (1, 2) Â· CRX Â· CUTL1 Â· DBX (1, 2) Â· DLX (3, 4, 5) Â· EMX (1, 2) Â· EN (1, 2) Â· FHL (1, 2, 3) Â· HESX1 Â· HHEX Â· HLX Â· Homeobox (A1, A2, A3, A4, A5, A7, A9, A10, A11, A13, B1, B2, B3, B4, B5, B6, B7, B8, B9, B13, C4, C5, C6, C8, C9, C10, C11, C12, C13, D1, D3, D4, D8, D9, D10, D11, D12, D13) Â· HOPX Â· IRX (1, 2, 3, 4, 5, 6, MKX) Â· LMX (1A, 1B) Â· MEIS (1, 2) Â· MEOX2 Â· MNX1 Â· MSX (1, 2) Â· NANOG Â· NKX (2-1, 2-2, 2-3, 2-5, 3-1, 3-2, 6-1, 6-2) Â· NOBOX Â· PBX (1, 2, 3) Â· PHF (1, 3, 6, 8, 10, 16, 17, 20, 21A) Â· PHOX (2A, 2B) Â· PITX (1, 2, 3) Â· POU domain (PIT-1, BRN-3: A, B, C, Octamer transcription factor: 1, 2, 3/4, 6, 7, 11) Â· OTX (1, 2) Â· PDX1 Â· SATB2 Â· SHOX2 Â· SIX (1, 2, 3, 4, 5) Â· VAX1 Â· ZEB (1, 2)

(3.2) Paired box	PAX (1, 2, 3, 4, 5, 6, 7, 8, 9)

(3.3) Fork head / winged helix	E2F (1, 2, 3, 4, 5) Â· FOX proteins (A1, A2, A3, C1, C2, D3, D4, E1, E3, F1, G1, H1, I1, J1, J2, K1, K2, L2, M1, N1, N3, O1, O3, O4, P1, P2, P3, P4)

(3.4) Heat Shock Factors	HSF (1, 2, 4)

(3.5) Tryptophan clusters	ELF (2, 4, 5) Â· EGF Â· ELK (1, 3, 4) Â· ERF Â· ETS (1, 2, ERG, SPIB) Â· ETV (1, 4, 5, 6) Â· FLI1 Â· Interferon regulatory factors (1, 2, 3, 4, 5, 6, 7, 8) Â· MYB Â· MYBL2

(3.6) TEA domain	transcriptional enhancer factor (1, 2, 3, 4)

(4) Î²-Scaffold factors with minor groove contacts

(4.1) Rel homology region	NF-ÎºB (NFKB1, NFKB2, REL, RELA, RELB) Â· NFAT (C1, C2, C3, C4, 5)

(4.2) STAT	STAT (1, 2, 3, 4, 5, 6)

(4.3) p53	p53 Â· TBX (1, 2, 3, 5, 19, 21, 22, Brachyury, TBR1, TBR2) Â· TP63

(4.4) MADS box	Mef2 (A, B, C, D) Â· SRF

(4.6) TATA binding proteins	TBP Â· TBPL1

(4.7) High-mobility group	BBX Â· HMGB (1, 2, 3, 4) Â· HMGN (1, 2, 3, 4) Â· HNF (1A, 1B) Â· LEF1 Â· SOX (1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 18, 21) Â· SRY Â· SSRP1 Â· TCF (3, 4) Â· TOX (1, 2, 3, 4)

(4.9) Grainyhead	TFCP2

(4.10) Cold-shock domain	CSDA, YBX1

(4.11) Runt	CBF (CBFA2T2, CBFA2T3, RUNX1, RUNX2, RUNX3, RUNX1T1)

(0) Other transcription factors

(0.2) HMGI(Y)	HMGA (1, 2) Â· HBP1

(0.3) Pocket domain	Rb Â· RBL1 Â· RBL2

(0.5) AP-2/EREBP-related factors	Apetala 2 Â· EREBP Â· B3

(0.6) Miscellaneous	ARID (1A, 1B, 2, 3A, 3B, 4A) Â· CAP Â· IFI (16, 35) Â· MLL (2, 3, T1) Â· MNDA Â· NFY (A, B, C) Â· Rho/Sigma

see also transcription factor/coregulator deficiencies
B bsyn: dna (repl, cycl, reco, repr) Â· tscr (fact, tcrg, nucl, rnat, rept, ptts) Â· tltn (risu, pttl, nexn) Â· dnab, rnab/runp Â· stru (domn, 1Â°, 2Â°, 3Â°, 4Â°)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

zinc-finger binding domain of transposase IS66 Provide feedback

This is a zinc-finger region of the N-terminus of the insertion element IS66 transposase.

Literature references

Han CG, Shiga Y, Tobe T, Sasakawa C, Ohtsubo E; , J Bacteriol 2001;183:4296-4304.: Structural and functional characterization of IS679 and IS66-family elements. PUBMED:11418571 EPMC:11418571

Internal database links

Similarity to PfamA using HHSearch:

Mut7-C zf-ISL3

External database links

PANDIT:	PF13005
Pseudofam:	PF13005
SYSTERS:	zf-IS66

This tab holds annotation information from the InterPro database.

InterPro entry IPR024474

This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [PUBMED:11418571].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (190)	Full (3219)	Representative proteomes				NCBI (2843)	Meta (332)
	Seed (190)	Full (3219)	RP15 (111)	RP35 (286)	RP55 (407)	RP75 (565)	NCBI (2843)	Meta (332)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (190)	Full (3219)	Representative proteomes				NCBI (2843)	Meta (332)
	Seed (190)	Full (3219)	RP15 (111)	RP35 (286)	RP55 (407)	RP75 (565)	NCBI (2843)	Meta (332)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (190)	Full (3219)	Representative proteomes				NCBI (2843)	Meta (332)
	Seed (190)	Full (3219)	RP15 (111)	RP35 (286)	RP55 (407)	RP75 (565)	NCBI (2843)	Meta (332)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

IS-finder

Previous IDs:

HTH_Tnp_IS66;

Type:

Domain

Author:

Coggill P

Number in seed:

190

Number in full:

3219

Average length of the domain:

45.40 aa

Average identity of full alignment:

39 %

Average coverage of the sequence by the domain:

10.71 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.0	20.0
Trusted cut-off	20.0	20.0
Noise cut-off	19.9	19.8

Model length:

47

Family (HMM) version:

2

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: zf-IS66 (PF13005)

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Summary: zinc-finger binding domain of transposase IS66

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Helix-turn-helix Edit Wikipedia article

Contents

[edit] Discovery

[edit] Function

[edit] Classification of helix-turn-helix motifs

[edit] Tri-helical

[edit] Tetra-helical

[edit] Winged helix-turn-helix

[edit] Other modified helix-turn-helix motifs

[edit] See also

[edit] References

[edit] Further reading

[edit] External links

zinc-finger binding domain of transposase IS66 Provide feedback

Literature references

Internal database links

External database links

InterPro entry IPR024474

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree