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0  structures 5  species 0  interactions 264  sequences 9  architectures

Family: CUB_2 (PF02408)

Summary: CUB-like domain

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This is the Wikipedia entry entitled "CUB domain". More...

CUB domain Edit Wikipedia article

CUB domain
Identifiers
Symbol CUB
Pfam PF00431
InterPro IPR000859
PROSITE PDOC00758
SCOP 1sfp
SUPERFAMILY 1sfp
CDD cd00041

CUB domain is an evolutionarily conserved protein domain.

The CUB domain (for complement C1r/C1s, Uegf, Bmp1) is a structural motif of approximately 110 residues found almost exclusively in extracellular and plasma membrane-associated proteins, many of which are developmentally regulated.[1][2] These proteins are involved in a diverse range of functions, including complement activation, developmental patterning, tissue repair, axon guidance and angiogenesis, cell signalling, fertilisation, haemostasis, inflammation, neurotransmission, receptor-mediated endocytosis, and tumour suppression.[3] Many CUB-containing proteins are peptidases belonging to MEROPS peptidase families M12A (astacin) and S1A (chymotrypsin).

Examples[edit]

Proteins containing a CUB domain include:

  • Mammalian complement subcomponents C1s/C1r, which form the calcium-dependent complex C1, the first component of the classical pathway of the complement system.
  • Cricetidae sp. (Hamster) serine protease Casp, which degrades type I and IV collagen and fibronectin in the presence of calcium.
  • Mammalian complement-activating component of Ra-reactive factor (RARF), a protease that cleaves the C4 component of complement.
  • Vertebrate enteropeptidase (EC 3.4.21.9), a type II membrane protein of the intestinal brush border, which activates trypsinogen.
  • Vertebrate bone morphogenic protein 1 (BMP-1), a protein which induces cartilage and bone formation and expresses metalloendopeptidase activity.
  • Sea urchin blastula proteins BP10 and SpAN.
  • C. elegans hypothetical proteins F42A10.8 and R151.5.
  • Neuropilin (A5 antigen), a calcium-independent cell adhesion molecule that functions during the formation of certain neuronal circuits.
  • Fibropellins I and III from Strongylocentrotus purpuratus (Purple sea urchin).
  • Mammalian hyaluronate-binding protein TSG-6 (or PS4), a serum and growth factor induced protein.
  • Mammalian spermadhesins.
  • Xenopus laevis embryonic protein UVS.2, which is expressed during dorsoanterior development.

Several of the above proteins consist of a catalytic domain together with several CUB domains interspersed by calcium-binding EGF domains. Some CUB domains appear to be involved in oligomerisation and/or recognition of substrates and binding partners. For example, in the complement proteases, the CUB domains mediate dimerisation and binding to collagen-like regions of target proteins (e.g. C1q for C1r/C1s). The structure of CUB domains consists of a beta-sandwich with a jelly-roll fold. Almost all CUB domains contain four conserved cysteines that probably form two disulphide bridges (C1-C2, C3-C4). The CUB1 domains of C1s and Map19 have calcium-binding sites.[4]

Human genes encoding proteins containing this domain include:

References[edit]

  1. ^ Bork P, Beckmann G (May 1993). "The CUB domain. A widespread module in developmentally regulated proteins". J. Mol. Biol. 231 (2): 539–45. doi:10.1006/jmbi.1993.1305. PMID 8510165. 
  2. ^ Bork P (April 1991). "Complement components C1r/C1s, bone morphogenic protein 1 and Xenopus laevis developmentally regulated protein UVS.2 share common repeats". FEBS Lett. 282 (1): 9–12. doi:10.1016/0014-5793(91)80433-4. PMID 2026272. 
  3. ^ Perry SE, Robinson P, Melcher A, Quirke P, Bühring HJ, Cook GP, Blair GE (March 2007). "Expression of the CUB domain containing protein 1 (CDCP1) gene in colorectal tumour cells". FEBS Lett. 581 (6): 1137–42. doi:10.1016/j.febslet.2007.02.025. PMID 17335815. 
  4. ^ Blanc G, Font B, Eichenberger D, Moreau C, Ricard-Blum S, Hulmes DJ, Moali C (June 2007). "Insights into how CUB domains can exert specific functions while sharing a common fold: conserved and specific features of the CUB1 domain contribute to the molecular basis of procollagen C-proteinase enhancer-1 activity". J. Biol. Chem. 282 (23): 16924–33. doi:10.1074/jbc.M701610200. PMID 17446170. 

This article incorporates text from the public domain Pfam and InterPro IPR000858

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

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CUB-like domain Provide feedback

This is a family of hypothetical C. elegans proteins. The aligned region has no known function nor do any of the proteins which possess it. However, this domain is related to the CUB domain.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003366

This domain is found in a family of hypothetical Caenorhabditis elegans proteins. The aligned region has no known function nor do any of the proteins which possess it. However, this domain is related to the CUB domain (INTERPRO). The aligned region is approximately 130 amino acids long and contains two conserved cysteine residues.

Domain organisation

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

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Pfam Clan

This family is a member of clan CUB (CL0164), which contains the following 2 members:

CUB CUB_2

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...

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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
(24)
Full
(264)
Representative proteomes NCBI
(312)
Meta
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RP15
(50)
RP35
(67)
RP55
(250)
RP75
(250)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(24)
Full
(264)
Representative proteomes NCBI
(312)
Meta
(0)
RP15
(50)
RP35
(67)
RP55
(250)
RP75
(250)
Alignment:
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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
(24)
Full
(264)
Representative proteomes NCBI
(312)
Meta
(0)
RP15
(50)
RP35
(67)
RP55
(250)
RP75
(250)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped 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.

Pfam alignments:

HMM logo

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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 View help on the curation process

Seed source: Pfam-B_1716 (release 5.4)
Previous IDs: DUF141;
Type: Domain
Author: Bashton M, Bateman A
Number in seed: 24
Number in full: 264
Average length of the domain: 113.70 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 25.57 %

HMM information View help on HMM parameters

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 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 120
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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