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PDBsum entry 1u5m

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Structural protein PDB id
1u5m
Jmol
Contents
Protein chain
73 a.a. *
* Residue conservation analysis
PDB id:
1u5m
Name: Structural protein
Title: Structure of a chordin-like cysteine-rich repeat (vwc module) from collagen iia
Structure: Alpha 1 type ii collagen isoform 1. Chain: a. Fragment: exon2. Synonym: collagen ii, alpha-1 polypeptide. Cartilage collagen. Chondrocalcin, included. Col11a3, formerly. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: col2a1. Expressed in: pichia pastoris. Expression_system_taxid: 4922.
NMR struc: 20 models
Authors: J.M.O'Leary,J.M.Hamilton,C.M.Deane,N.V.Valeyev,L.J.Sandell, A.K.Downing
Key ref:
J.M.O'Leary et al. (2004). Solution structure and dynamics of a prototypical chordin-like cysteine-rich repeat (von Willebrand Factor type C module) from collagen IIA. J Biol Chem, 279, 53857-53866. PubMed id: 15466413 DOI: 10.1074/jbc.M409225200
Date:
28-Jul-04     Release date:   05-Oct-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02458  (CO2A1_HUMAN) -  Collagen alpha-1(II) chain
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1487 a.a.
73 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 

 
DOI no: 10.1074/jbc.M409225200 J Biol Chem 279:53857-53866 (2004)
PubMed id: 15466413  
 
 
Solution structure and dynamics of a prototypical chordin-like cysteine-rich repeat (von Willebrand Factor type C module) from collagen IIA.
J.M.O'Leary, J.M.Hamilton, C.M.Deane, N.V.Valeyev, L.J.Sandell, A.K.Downing.
 
  ABSTRACT  
 
Chordin-like cysteine-rich (CR) repeats (also referred to as von Willebrand factor type C (VWC) modules) have been identified in approximately 200 extracellular matrix proteins. These repeats, named on the basis of amino acid conservation of 10 cysteine residues, have been shown to bind members of the transforming growth factor-beta (TGF-beta) superfamily and are proposed to regulate growth factor signaling. Here we describe the intramolecular disulfide bonding, solution structure, and dynamics of a prototypical chordin-like CR repeat from procollagen IIA (CR(ColIIA)), which has been previously shown to bind TGF-beta1 and bone morphogenetic protein-2. The CR(ColIIA) structure manifests a two sub-domain architecture tethered by a flexible linkage. Initial structures were calculated using RosettaNMR, a de novo prediction method, and final structure calculations were performed using CANDID within CYANA. The N-terminal region contains mainly beta-sheet and the C-terminal region is more irregular with the fold constrained by disulfide bonds. Mobility between the N- and C-terminal sub-domains on a fast timescale was confirmed using NMR relaxation measurements. We speculate that the mobility between the two sub-domains may decrease upon ligand binding. Structure and sequence comparisons have revealed an evolutionary relationship between the N-terminal sub-domain of the CR module and the fibronectin type 1 domain, suggesting that these domains share a common ancestry. Based on the previously reported mapping of fibronectin binding sites for vascular endothelial growth factor to regions containing fibronectin type 1 domains, we discuss the possibility that this structural homology might also have functional relevance.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Multiple sequence alignment of CR repeat sequences from the SWISS-PROT data base from procollagen IIA, chordin, connective tissue growth factor, neuralin, and Cyr61. Residues Cys34-Cys89 of the CR[ColIIA] sequence, corresponding to the Pfam entry for the VWC domain, are shown. Sequences were aligned using ClustalX (71).
Figure 5.
FIG. 5. Comparison of the N-terminal sub-domain of CR[ColIIA] (shown in turquoise) and fibronectin type 1 (shown in pink) domains. A, structural alignment of the N-terminal domain of CR[CoIIIA] and the N-terminal domain of 1FBR (a representative structure of the fibronectin type 1 domain) based on the backbone atoms of 40 residues (r.m.s.d. = 2.0 Å). Cysteines in the N-terminal domain of CR[CoIIIA] domain are highlighted in black excluding Cys52, which is not conserved in fibronectin domains but forms a disulfide bond to the second domain in CR[CoIIIA]. B, multiple sequence alignment of the N-terminal sub-domain of CR[ColIIA] and FN1 domain sequences from fibronectin. For the CR[ColIIA] sequence, residues Ala^31-Ile^67 are shown in the alignment.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 53857-53866) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20831445 I.Azimi, J.W.Wong, and P.J.Hogg (2011).
Control of mature protein function by allosteric disulfide bonds.
  Antioxid Redox Signal, 14, 113-126.  
21284856 Q.Wang, W.Usinger, B.Nichols, J.Gray, L.Xu, T.W.Seeley, M.Brenner, G.Guo, W.Zhang, N.Oliver, A.Lin, and D.Yeowell (2011).
Cooperative interaction of CTGF and TGF-β in animal models of fibrotic disease.
  Fibrogenesis Tissue Repair, 4, 4.  
21221697 R.A.Barrero, M.Bellgard, and X.Zhang (2011).
Diverse approaches to achieving grain yield in wheat.
  Funct Integr Genomics, 11, 37-48.  
20116835 L.M.Maurer, B.R.Tomasini-Johansson, and D.F.Mosher (2010).
Emerging roles of fibronectin in thrombosis.
  Thromb Res, 125, 287-291.  
19424823 K.P.Holbourn, B.Perbal, and K.Ravi Acharya (2009).
Proteins on the catwalk: modelling the structural domains of the CCN family of proteins.
  J Cell Commun Signal, 3, 25-41.  
19630758 P.J.Hogg (2009).
Contribution of allosteric disulfide bonds to regulation of hemostasis.
  J Thromb Haemost, 7, 13-16.  
19706610 Y.Liu, and D.F.Mosher (2009).
Interactions among stalk modules of thrombospondin-1.
  J Biol Chem, 284, 28563-28570.  
18193164 C.B.Carlson, J.Lawler, and D.F.Mosher (2008).
Structures of thrombospondins.
  Cell Mol Life Sci, 65, 672-686.  
18789696 K.P.Holbourn, K.R.Acharya, and B.Perbal (2008).
The CCN family of proteins: structure-function relationships.
  Trends Biochem Sci, 33, 461-473.  
  18391434 L.Y.Qiu, J.L.Zhang, A.Kotzsch, W.Sebald, and T.D.Mueller (2008).
Crystallization and preliminary X-ray analysis of the complex of the first von Willebrand type C domain bound to bone morphogenetic protein 2.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 307-312.  
  19690637 J.D.Birmingham, V.Vilim, and V.B.Kraus (2007).
Collagen biomarkers for arthritis applications.
  Biomark Insights, 1, 61-76.  
17018525 A.Oganesian, S.Au, J.A.Horst, L.C.Holzhausen, A.J.Macy, J.M.Pace, and P.Bornstein (2006).
The NH2-terminal propeptide of type I procollagen acts intracellularly to modulate cell function.
  J Biol Chem, 281, 38507-38518.  
16444707 C.C.Wang, J.H.Chen, S.H.Yin, and W.J.Chuang (2006).
Predicting the redox state and secondary structure of cysteine residues in proteins using NMR chemical shifts.
  Proteins, 63, 219-226.  
16453132 C.Fan, Y.Xing, H.Mao, T.Lu, B.Han, C.Xu, X.Li, and Q.Zhang (2006).
GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein.
  Theor Appl Genet, 112, 1164-1171.  
16407063 K.Tan, M.Duquette, J.H.Liu, R.Zhang, A.Joachimiak, J.H.Wang, and J.Lawler (2006).
The structures of the thrombospondin-1 N-terminal domain and its complex with a synthetic pentameric heparin.
  Structure, 14, 33-42.
PDB codes: 1z78 1za4 2erf
17082774 N.V.Lee, M.Sato, D.S.Annis, J.A.Loo, L.Wu, D.F.Mosher, and M.L.Iruela-Arispe (2006).
ADAMTS1 mediates the release of antiangiogenic polypeptides from TSP1 and 2.
  EMBO J, 25, 5270-5283.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.