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PDBsum entry 1x2t

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protein ligands metals Protein-protein interface(s) links
Protein binding PDB id
1x2t
Jmol PyMol
Contents
Protein chains
129 a.a. *
123 a.a. *
Ligands
1PE ×2
Metals
_CA ×4
Waters ×568
* Residue conservation analysis
PDB id:
1x2t
Name: Protein binding
Title: Crystal structure of habu ix-bp at ph 6.5
Structure: Coagulation factor ix/x-binding protein a chain. Chain: a, c. Coagulation factor ix/factor x-binding protein b chain. Chain: b, d. Synonym: ix/x-bp
Source: Trimeresurus flavoviridis. Organism_taxid: 88087. Secretion: venom. Secretion: venom
Biol. unit: Dimer (from PQS)
Resolution:
1.72Å     R-factor:   0.191     R-free:   0.222
Authors: N.Suzuki,Z.Fujimoto,T.Morita,A.Fukamizu,H.Mizuno
Key ref:
N.Suzuki et al. (2005). pH-Dependent structural changes at Ca(2+)-binding sites of coagulation factor IX-binding protein. J Mol Biol, 353, 80-87. PubMed id: 16165155 DOI: 10.1016/j.jmb.2005.08.018
Date:
26-Apr-05     Release date:   04-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7LZ71  (IXA_PROFL) -  Snaclec coagulation factor IX-binding protein subunit A
Seq:
Struc:
129 a.a.
129 a.a.
Protein chains
Pfam   ArchSchema ?
P23807  (IXXB_PROFL) -  Snaclec coagulation factor IX/factor X-binding protein subunit B
Seq:
Struc:
146 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biochemical function     metal ion binding     2 terms  

 

 
DOI no: 10.1016/j.jmb.2005.08.018 J Mol Biol 353:80-87 (2005)
PubMed id: 16165155  
 
 
pH-Dependent structural changes at Ca(2+)-binding sites of coagulation factor IX-binding protein.
N.Suzuki, Z.Fujimoto, T.Morita, A.Fukamizu, H.Mizuno.
 
  ABSTRACT  
 
Coagulation factor IX-binding protein, isolated from Trimeresurus flavoviridis (IX-bp), is a C-type lectin-like protein. It is an anticoagulant consisting of homologous subunits, A and B. Each subunit has a Ca(2+)-binding site with a unique affinity (K(d) values of 14muM and 130muM at pH 7.5). These binding characteristics are pH-dependent and, under acidic conditions, the Ca(2+) binding of the low-affinity site was reduced considerably. In order to identify which site has high affinity and to investigate the pH-dependent Ca(2+) release mechanism, we have determined the crystal structures of IX-bp at pH 6.5 and pH 4.6 (apo form), and compared the Ca(2+)-binding sites with each other and with those of the solved structures under alkaline conditions; pH 7.8 and pH 8.0 (complexed form). At pH 6.5, Glu43 in the Ca(2+)-binding site of subunit A displayed two conformations. One (minor) is that in the alkaline state, and the other (major) is that at pH 4.6. However, the corresponding Gln43 residue of subunit B is in only a single conformation, which is almost identical with that in the alkaline state. At pH 4.6, Glu43 of subunit A adopts a conformation similar to that of the major conformer observed at pH 6.5, while Gln43 of subunit B assumes a new conformation, and both Ca(2+) positions are occupied by water molecules. These results showed that Glu43 of subunit A is much more sensitive to protonation than Gln43 of subunit B, and the conformational change of Glu43 occurs around pH6.5, which may correspond to the step of Ca(2+) release.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereoviews of ball-and stick models of the Ca^2+-binding sites of (a) subunit A and (b) subunit B. The models at pH 8.0, pH 6.5 and pH 4.6 are shown in cyan, orange and magenta, respectively. Dotted lines in grey and green indicate Ca^2+ coordination and hydrogen bonds, respectively.
Figure 3.
Figure 3. Close-up views of pH-dependent conformational changes of (a) GluA43 and (b) GlnB43 coordinating to the Ca^2+. Conformational changes are shown by the rotation of torsion angles. The models at pH 8.0, pH 6.5 and pH 4.6 are shown in cyan, orange and magenta, respectively.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 80-87) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18849817 H.Lier, H.Krep, S.Schroeder, and F.Stuber (2008).
Preconditions of hemostasis in trauma: a review. The influence of acidosis, hypocalcemia, anemia, and hypothermia on functional hemostasis in trauma.
  J Trauma, 65, 951-960.  
17962412 G.M.Besserer, M.Ottolia, D.A.Nicoll, V.Chaptal, D.Cascio, K.D.Philipson, and J.Abramson (2007).
The second Ca2+-binding domain of the Na+ Ca2+ exchanger is essential for regulation: crystal structures and mutational analysis.
  Proc Natl Acad Sci U S A, 104, 18467-18472.
PDB codes: 2qvk 2qvm
17096106 H.Lier, S.Kampe, and S.Schröder (2007).
[Prerequisites of a functional haemostasis. What must be considered at the scene of an accident, in the emergency room and during an operation?]
  Anaesthesist, 56, 239-251.  
16782791 P.J.Kundrotas, and E.Alexov (2006).
Electrostatic properties of protein-protein complexes.
  Biophys J, 91, 1724-1736.  
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.

 

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