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Transferase PDB id
1ggy
Jmol
Contents
Protein chains
702 a.a. *
Metals
_YB ×8
Waters ×265
* Residue conservation analysis
PDB id:
1ggy
Name: Transferase
Title: Human factor xiii with ytterbium bound in the ion site
Structure: Protein (coagulation factor xiii). Chain: a, b. Fragment: full length. Engineered: yes. Other_details: ytterbium soaked into crystal
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.188     R-free:   0.281
Authors: B.A.Fox,V.C.Yee,L.C.Pederson,I.L.Trong,P.D.Bishop,R.E.Stenka D.C.Teller
Key ref:
B.A.Fox et al. (1999). Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography. J Biol Chem, 274, 4917-4923. PubMed id: 9988734 DOI: 10.1074/jbc.274.8.4917
Date:
23-Jul-98     Release date:   16-Feb-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00488  (F13A_HUMAN) -  Coagulation factor XIII A chain
Seq:
Struc: 		 
Seq:
Struc: 		732 a.a.
702 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.3.2.13  - Protein-glutamine gamma-glutamyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein glutamine + alkylamine = protein N5-alkylglutamine + NH3
Protein glutamine
 + alkylamine
 = protein N(5)-alkylglutamine
 + NH(3)
      Cofactor: Calcium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     wound healing   5 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.274.8.4917 J Biol Chem 274:4917-4923 (1999)
PubMed id: 9988734  
 
 
Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography.
B.A.Fox, V.C.Yee, L.C.Pedersen, I.Le Trong, P.D.Bishop, R.E.Stenkamp, D.C.Teller.
 
  ABSTRACT  
 
The presence or absence of calcium determines the activation, activity, oligomerization, and stability of blood coagulation factor XIII. To explore these observed effects, we have determined the x-ray crystal structure of recombinant factor XIII A2 in the presence of calcium, strontium, and ytterbium. The main calcium binding site within each monomer involves the main chain oxygen atom of Ala-457, and also the side chains from residues Asn-436, Asp-438, Glu-485, and Glu-490. Calcium and strontium bind in the same location, while ytterbium binds several angstroms removed. A novel ytterbium binding site is also found at the dimer two-fold axis, near residues Asp-270 and Glu-272, and this site may be related to the reported inhibition by lanthanide metals (Achyuthan, K. E., Mary, A., and Greenberg, C. S. (1989) Biochem. J. 257, 331-338). The overall structure of ion-bound factor XIII is very similar to the previously determined crystal structures of factor XIII zymogen, likely due to the constraints of this monoclinic crystal form. We have merged the three independent sets of water molecules in the structures to determine which water molecules are conserved and possibly structurally significant.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Overall structure of the factor XIII dimer. Panel A is the dimer looking down the two-fold axis. The domains, activation peptide (AP), and N and C termini of one monomer are labeled. Panel B shows one monomer, rotated 90° with the domains, N terminus, active site (AS), and ion sites labeled. For both views, three unique spheres are also shown: novel ytterbium site on the dimer two-fold axis (medium gray), active site (light gray), and main ion site (dark gray). 		Figure 6.
Fig. 6. Structurally significant water molecule. Water 6059S is shown as a sphere with several secondary structure elements nearby. The residues near this water are also shown. The active site residue His-373 and calcium binding ligand Ala-457 are shown.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 4917-4923) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20880254 I.Komáromi, Z.Bagoly, and L.Muszbek (2011).
Factor XIII: novel structural and functional aspects.
  J Thromb Haemost, 9, 9.  
19241467 M.L.Herman, S.Farasat, P.J.Steinbach, M.H.Wei, O.Toure, P.Fleckman, P.Blake, S.J.Bale, and J.R.Toro (2009).
Transglutaminase-1 gene mutations in autosomal recessive congenital ichthyosis: summary of mutations (including 23 novel) and modeling of TGase-1.
  Hum Mutat, 30, 537-547.  
18544639 K.A.Johnson, D.M.Rose, and R.A.Terkeltaub (2008).
Factor XIIIA mobilizes transglutaminase 2 to induce chondrocyte hypertrophic differentiation.
  J Cell Sci, 121, 2256-2264.  
18833291 S.Gong, and T.L.Blundell (2008).
Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures.
  PLoS Comput Biol, 4, e1000179.  
16782800 A.De Riso, D.L.Jenson, and B.A.Barry (2006).
Calcium exchange and structural changes during the photosynthetic oxygen evolving cycle.
  Biophys J, 91, 1999-2008.  
15619637 C.Steegborn, T.N.Litvin, L.R.Levin, J.Buck, and H.Wu (2005).
Bicarbonate activation of adenylyl cyclase via promotion of catalytic active site closure and metal recruitment.
  Nat Struct Mol Biol, 12, 32-37.
PDB codes: 1wc0 1wc1 1wc3 1wc4 1wc5 1wc6
15456491 A.Vysokovsky, R.Saxena, M.Landau, A.Zivelin, R.Eskaraev, N.Rosenberg, U.Seligsohn, and A.Inbal (2004).
Seven novel mutations in the factor XIII A-subunit gene causing hereditary factor XIII deficiency in 10 unrelated families.
  J Thromb Haemost, 2, 1790-1797.  
12563291 L.Lorand, and R.M.Graham (2003).
Transglutaminases: crosslinking enzymes with pleiotropic functions.
  Nat Rev Mol Cell Biol, 4, 140-156.  
11980702 B.Ahvazi, H.C.Kim, S.H.Kee, Z.Nemes, and P.M.Steinert (2002).
Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions changes structure for activation.
  EMBO J, 21, 2055-2067.
PDB codes: 1l9m 1l9n
12368090 L.Fesus, and M.Piacentini (2002).
Transglutaminase 2: an enigmatic enzyme with diverse functions.
  Trends Biochem Sci, 27, 534-539.  
11867708 S.Liu, R.A.Cerione, and J.Clardy (2002).
Structural basis for the guanine nucleotide-binding activity of tissue transglutaminase and its regulation of transamidation activity.
  Proc Natl Acad Sci U S A, 99, 2743-2747.
PDB code: 1kv3
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.