Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
584  structures 6041  species 32  interactions 71985  sequences 895  architectures

Clan: PDDEXK (CL0236)

Summary

PD-(D/E)XK nuclease superfamily Add an annotation

This clan includes a large number of nuclease families related to holliday junction resolvases [1,2].

This clan contains 123 families and the total number of domains in the clan is 71985. The clan was built by A Bateman.

Literature references

  1. Aravind L, Makarova KS, Koonin EV; , Nucleic Acids Res. 2000;28:3417-3432.: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. PUBMED:10982859 EPMC:10982859
  2. Feder M, Bujnicki JM; , BMC Genomics. 2005;6:21-21.: Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. PUBMED:15720711 EPMC:15720711
  3. Knizewski L, Kinch L, Grishin NV, Rychlewski L, Ginalski K; , J Virol. 2006;80:2575-2577.: Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease. PUBMED:16474163 EPMC:16474163
  4. Kinch LN, Ginalski K, Rychlewski L, Grishin NV; , Nucleic Acids Res. 2005;33:3598-3605.: Identification of novel restriction endonuclease-like fold families among hypothetical proteins. PUBMED:15972856 EPMC:15972856
  5. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;, Nucleic Acids Res. 2012;40:7016-7045.: Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. PUBMED:22638584 EPMC:22638584

Members

This clan contains the following 123 member families:

BamHI BpuSI_N Bse634I BsuBI_PstI_RE Cas_APE2256 Cas_Cas02710 Cas_Cas4 Cas_Csm6 Cas_NE0113 CoiA Dna2 DpnII DRP DUF1016 DUF1052 DUF1064 DUF1626 DUF1703 DUF1780 DUF1853 DUF1887 DUF2034 DUF2130 DUF234 DUF2726 DUF2800 DUF2887 DUF3799 DUF3883 DUF4143 DUF4263 DUF4420 DUF506 DUF524 DUF559 DUF790 DUF91 DUF911 EcoRI EcoRII-C eIF-3_zeta Endonuc-BglII Endonuc-BsobI Endonuc-EcoRV Endonuc-FokI_C Endonuc-HincII Endonuc-MspI Endonuc-PvuII Endonuc_BglI Endonuc_Holl ERCC4 Exo5 Herpes_alk_exo Herpes_UL24 Hjc HSDR_N HSDR_N_2 L_protein_N McrBC Mrr_cat Mrr_cat_2 MutH MvaI_BcnI NaeI NARG2_C NERD NgoMIV_restric NotI PDDEXK_1 PDDEXK_2 PDDEXK_3 PDDEXK_4 PDDEXK_5 Pet127 Phage_endo_I R-HINP1I RAI1 RAP RE_AlwI RE_ApaLI RE_Bpu10I RE_Bsp6I RE_CfrBI RE_Eco47II RE_EcoO109I RE_HaeII RE_HindIII RE_HindVP RE_HpaII RE_LlaJI RE_LlaMI RE_MjaI RE_NgoBV RE_NgoPII RE_SacI RE_ScaI RE_SinI RE_TaqI RE_TdeIII RE_XamI RE_XcyI RecU RestrictionMunI RestrictionSfiI RmuC RNA_pol_Rpb5_N Sen15 SfsA TBPIP_N ThaI Tn7_Tnp_TnsA_N Transposase_31 tRNA_int_endo Tsp45I Uma2 UPF0102 VirArc_Nuclease VRR_NUC Vsr XhoI XisH YaeQ YqaJ

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

Loading domain graphics...

Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
PDDEXK_1 (PF12705) 8235 (11.4%) View
Uma2 (PF05685) 4083 (5.7%) View
HSDR_N (PF04313) 3819 (5.3%) View
Transposase_31 (PF04754) 3243 (4.5%) View
UPF0102 (PF02021) 3091 (4.3%) View
DUF4143 (PF13635) 2818 (3.9%) View
RmuC (PF02646) 2678 (3.7%) View
Mrr_cat (PF04471) 2560 (3.6%) View
PDDEXK_2 (PF12784) 2282 (3.2%) View
DUF1016 (PF06250) 1895 (2.6%) View
NERD (PF08378) 1767 (2.5%) View
SfsA (PF03749) 1762 (2.4%) View
DUF559 (PF04480) 1749 (2.4%) View
YqaJ (PF09588) 1553 (2.2%) View
HSDR_N_2 (PF13588) 1412 (2.0%) View
VRR_NUC (PF08774) 1394 (1.9%) View
DUF1703 (PF08011) 1376 (1.9%) View
RecU (PF03838) 1337 (1.9%) View
ERCC4 (PF02732) 1301 (1.8%) View
CoiA (PF06054) 1177 (1.6%) View
Cas_Cas4 (PF01930) 1113 (1.5%) View
Vsr (PF03852) 1075 (1.5%) View
YaeQ (PF07152) 1039 (1.4%) View
MutH (PF02976) 953 (1.3%) View
McrBC (PF10117) 909 (1.3%) View
DUF2726 (PF10881) 880 (1.2%) View
tRNA_int_endo (PF01974) 852 (1.2%) View
DUF91 (PF01939) 795 (1.1%) View
DUF2130 (PF09903) 737 (1.0%) View
DUF3883 (PF13020) 729 (1.0%) View
DUF234 (PF03008) 702 (1.0%) View
RAP (PF08373) 594 (0.8%) View
Tn7_Tnp_TnsA_N (PF08722) 557 (0.8%) View
DUF2800 (PF10926) 496 (0.7%) View
RNA_pol_Rpb5_N (PF03871) 436 (0.6%) View
DUF1064 (PF06356) 417 (0.6%) View
DUF1853 (PF08907) 413 (0.6%) View
PDDEXK_3 (PF13366) 398 (0.6%) View
eIF-3_zeta (PF05091) 378 (0.5%) View
RAI1 (PF08652) 357 (0.5%) View
PDDEXK_4 (PF14281) 355 (0.5%) View
DUF3799 (PF12684) 347 (0.5%) View
L_protein_N (PF15518) 334 (0.5%) View
RE_ApaLI (PF09499) 327 (0.5%) View
Dna2 (PF08696) 301 (0.4%) View
DUF506 (PF04720) 299 (0.4%) View
DRP (PF06044) 296 (0.4%) View
DUF1887 (PF09002) 279 (0.4%) View
Mrr_cat_2 (PF13156) 260 (0.4%) View
DUF1052 (PF06319) 250 (0.3%) View
Exo5 (PF09810) 244 (0.3%) View
DpnII (PF04556) 239 (0.3%) View
DUF2887 (PF11103) 232 (0.3%) View
Herpes_alk_exo (PF01771) 226 (0.3%) View
DUF524 (PF04411) 222 (0.3%) View
Sen15 (PF09631) 217 (0.3%) View
Cas_Csm6 (PF09659) 211 (0.3%) View
Hjc (PF01870) 183 (0.3%) View
DUF2034 (PF10356) 178 (0.2%) View
RE_AlwI (PF09491) 173 (0.2%) View
Herpes_UL24 (PF01646) 158 (0.2%) View
Pet127 (PF08634) 147 (0.2%) View
continued
Pfam family Num. domains Alignment
DUF790 (PF05626) 146 (0.2%) View
EcoRII-C (PF09019) 145 (0.2%) View
DUF4420 (PF14390) 142 (0.2%) View
XisH (PF08814) 139 (0.2%) View
DUF4263 (PF14082) 136 (0.2%) View
BsuBI_PstI_RE (PF06616) 135 (0.2%) View
DUF1626 (PF07788) 128 (0.2%) View
Cas_APE2256 (PF09651) 119 (0.2%) View
Cas_Cas02710 (PF09670) 109 (0.2%) View
Cas_NE0113 (PF09623) 107 (0.1%) View
RE_HpaII (PF09561) 103 (0.1%) View
NARG2_C (PF10505) 96 (0.1%) View
RE_LlaJI (PF09563) 86 (0.1%) View
MvaI_BcnI (PF15515) 77 (0.1%) View
Endonuc_Holl (PF10107) 76 (0.1%) View
Endonuc-BglII (PF09195) 74 (0.1%) View
DUF911 (PF06023) 70 (0.1%) View
RE_Eco47II (PF09553) 64 (0.1%) View
Phage_endo_I (PF05367) 64 (0.1%) View
RE_NgoPII (PF09521) 62 (0.1%) View
NgoMIV_restric (PF09015) 56 (0.1%) View
DUF1780 (PF08682) 56 (0.1%) View
RE_TdeIII (PF09520) 54 (0.1%) View
RE_EcoO109I (PF14511) 53 (0.1%) View
NotI (PF12183) 53 (0.1%) View
EcoRI (PF02963) 52 (0.1%) View
RE_NgoBV (PF09564) 50 (0.1%) View
XhoI (PF04555) 48 (0.1%) View
RE_MjaI (PF09568) 42 (0.1%) View
RE_HindVP (PF09519) 41 (0.1%) View
Endonuc-EcoRV (PF09233) 40 (0.1%) View
RE_CfrBI (PF09516) 36 (0.1%) View
Tsp45I (PF06300) 36 (0.1%) View
NaeI (PF09126) 31 (0.0%) View
Endonuc-FokI_C (PF09254) 30 (0.0%) View
RE_XamI (PF09572) 29 (0.0%) View
RE_HaeII (PF09554) 29 (0.0%) View
Endonuc-BsobI (PF09194) 29 (0.0%) View
RE_HindIII (PF09518) 26 (0.0%) View
RE_Bpu10I (PF09549) 25 (0.0%) View
R-HINP1I (PF11463) 24 (0.0%) View
PDDEXK_5 (PF11645) 21 (0.0%) View
BamHI (PF02923) 18 (0.0%) View
RE_Bsp6I (PF09504) 17 (0.0%) View
RE_SinI (PF09570) 15 (0.0%) View
RE_ScaI (PF09569) 14 (0.0%) View
Endonuc-PvuII (PF09225) 14 (0.0%) View
TBPIP_N (PF15517) 13 (0.0%) View
VirArc_Nuclease (PF12187) 13 (0.0%) View
RE_TaqI (PF09573) 13 (0.0%) View
RE_XcyI (PF09571) 13 (0.0%) View
Bse634I (PF07832) 13 (0.0%) View
RE_SacI (PF09566) 10 (0.0%) View
Endonuc-HincII (PF09226) 10 (0.0%) View
Endonuc-MspI (PF09208) 10 (0.0%) View
RestrictionMunI (PF11407) 9 (0.0%) View
RE_LlaMI (PF09562) 7 (0.0%) View
RestrictionSfiI (PF11487) 6 (0.0%) View
BpuSI_N (PF15516) 4 (0.0%) View
Endonuc_BglI (PF14562) 4 (0.0%) View
ThaI (PF15514) 3 (0.0%) View
Total: 123 Total: 71985 Clan alignment
 

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

We could not retrieve a family relationship diagram for this clan.

Species distribution

Tree controls

Hide

This tree shows the occurrence of the domains in this clan across different species. More...

Loading...

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

Loading structure mapping...