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0  structures 447  species 0  interactions 936  sequences 50  architectures

Family: CHRD (PF07452)

Summary: CHRD domain

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This is the Wikipedia entry entitled "Chordin". More...

Chordin Edit Wikipedia article

CHRD domain
Identifiers
Symbol CHRD
Pfam PF07452
InterPro IPR010895
SMART SM00754
PROSITE PS50933
chordin
Identifiers
Symbol CHRD
Entrez 8646
HUGO 1949
OMIM 603475
RefSeq NM_003741
UniProt Q9H2X0
Other data
Locus Chr. 3 q27

Chordin is a bone morphogenetic protein antagonist composed of four small cysteine-rich domains, whose function is not known. Chordin was originally identified in Xenopus laevis as a key developmental protein that dorsalizes early vertebrate embryonic tissues.[1] The polypeptide is 941 amino acids long and 120 kDa large[2] and it dorsalizes the developing embryo by binding ventralizing TGFβ proteins such as bone morphogenetic proteins.[3] It may also play a role in organogenesis. There are five named isoforms of this protein that are produced by alternative splicing.[4]

In mice, Chordin is expressed in the node but not in the anterior visceral endoderm. It has been found to be required for forebrain development.[5] In developing mice that are deficient in both chordin and noggin, the head is nearly absent. This is significant because when only noggin is deficient there are mild defects but the head still forms.[6]

In humans, the chordin peptide is encoded by the CHRD gene.[7]

Chordin is also involved in avian gastrulation. It is expressed in the anterior cells of Koller's sickle, which form the anterior cells of the primitive streak, a key structure through which gastrulation occurs. [8]

References[edit]

  1. ^ Sasai Y, Lu B, Steinbeisser H, Geissert D, Gont LK, De Robertis EM (December 1994). "Xenopus chordin: a novel dorsalizing factor activated by organizer-specific homeobox genes". Cell 79 (5): 779–90. doi:10.1016/0092-8674(94)90068-X. PMC 3082463. PMID 8001117. 
  2. ^ Larraín J, Bachiller D, Lu B, Agius E, Piccolo S, De Robertis EM (February 2000). "BMP-binding modules in chordin: a model for signalling regulation in the extracellular space". Development 127 (4): 821–30. PMC 2280033. PMID 10648240. 
  3. ^ Pappano WN, Scott IC, Clark TG, Eddy RL, Shows TB, Greenspan DS (September 1998). "Coding sequence and expression patterns of mouse chordin and mapping of the cognate mouse chrd and human CHRD genes". Genomics 52 (2): 236–9. doi:10.1006/geno.1998.5474. PMID 9782094. 
  4. ^ Millet C, Lemaire P, Orsetti B, Guglielmi P, François V (August 2001). "The human chordin gene encodes several differentially expressed spliced variants with distinct BMP opposing activities". Mech. Dev. 106 (1–2): 85–96. doi:10.1016/S0925-4773(01)00423-3. PMID 11472837. 
  5. ^ Bachiller D, Klingensmith J, Kemp C, Belo JA, Anderson RM, May SR, McMahon JA, McMahon AP, Harland RM, Rossant J, De Robertis EM (February 2000). "The organizer factors Chordin and Noggin are required for mouse forebrain development". Nature 403 (6770): 658–61. doi:10.1038/35001072. PMID 10688202. 
  6. ^ Harris WA, Sanes DH, Reh TA (2011). Development of the Nervous System (Third ed.). Boston: Academic Press. p. 15. ISBN 0-12-374539-X. 
  7. ^ Smith M, Herrell S, Lusher M, Lako L, Simpson C, Wiestner A, Skoda R, Ireland M, Strachan T (1999). "Genomic organisation of the human chordin gene and mutation screening of candidate Cornelia de Lange syndrome genes". Hum. Genet. 105 (1–2): 104–11. doi:10.1007/s004390051070. PMID 10480362. 
  8. ^ Vasiev B, Balter A, Chaplain M, Glazier JA, Weijer CJ. Modeling gastrulation in the chick embryo: formation of the primitive streak. PLoS One. 2010;5:e10571. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010571


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CHRD domain Provide feedback

CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made. Its most conserved feature is a GE[I/L]RCG[V/I/L] motif towards its C-terminal end Most bacterial proteins in this family have only one CHRD domain, whereas it is found repeated in many eukaryotic proteins such as human chordin (Q9H2X0) and Drosophila SOG (Q24025). [1].

Literature references

  1. Hyvonen M; , Trends Biochem Sci 2003;28:470-473.: CHRD, a novel domain in the BMP inhibitor chordin, is also found in microbial proteins. PUBMED:13678956 EPMC:13678956


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010895

CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made [PUBMED:13678956].

Domain organisation

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Alignments

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  Seed
(101)
Full
(936)
Representative proteomes NCBI
(766)
Meta
(59)
RP15
(104)
RP35
(190)
RP55
(262)
RP75
(346)
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Format an alignment

  Seed
(101)
Full
(936)
Representative proteomes NCBI
(766)
Meta
(59)
RP15
(104)
RP35
(190)
RP55
(262)
RP75
(346)
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
(101)
Full
(936)
Representative proteomes NCBI
(766)
Meta
(59)
RP15
(104)
RP35
(190)
RP55
(262)
RP75
(346)
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.

Pfam alignments:

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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.

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Curation and family details

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Seed source: Hyvonen M
Previous IDs: none
Type: Domain
Author: Hyvonen M
Number in seed: 101
Number in full: 936
Average length of the domain: 117.80 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 54.16 %

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 24.1 24.1
Trusted cut-off 24.1 24.2
Noise cut-off 23.9 23.9
Model length: 119
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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