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PDBsum entry 2doh

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2doh
Jmol
Contents
Protein chains
165 a.a. *
24 a.a. *
Ligands
DIO
Waters ×313
* Residue conservation analysis
PDB id:
2doh
Name: Hydrolase
Title: The x-ray crystallographic structure of the angiogenesis inh angiostatin, bound a to a peptide from the group a streptoc surface protein pam
Structure: Angiostatin. Chain: x. Fragment: kringle 1,kringle 2 and kringle 3. Engineered: yes. Mutation: yes. Plasminogen-binding group a streptococcal m-like pam. Chain: c. Fragment: vek-30.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: plg. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Synthetic: yes. Other_details: vek-30 is an internal peptide within pam
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.210     R-free:   0.260
Authors: S.E.Cnudde,M.Prorok,F.J.Castellino,J.H.Geiger
Key ref:
S.E.Cnudde et al. (2006). X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcal surface protein PAM. Biochemistry, 45, 11052-11060. PubMed id: 16964966 DOI: 10.1021/bi060914j
Date:
29-Apr-06     Release date:   05-Dec-06    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00747  (PLMN_HUMAN) -  Plasminogen
Seq:
Struc:
 
Seq:
Struc:
810 a.a.
165 a.a.
Protein chain
Pfam   ArchSchema ?
P49054  (PAM_STRPY) -  Plasminogen-binding group A streptococcal M-like protein PAM (Fragment)
Seq:
Struc:
388 a.a.
24 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain X: E.C.3.4.21.7  - Plasmin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Lys-|-Xaa > Arg-|-Xaa; higher selectivity than trypsin. Converts fibrin into soluble products.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     blood coagulation   2 terms 
  Biochemical function     calcium ion binding     2 terms  

 

 
DOI no: 10.1021/bi060914j Biochemistry 45:11052-11060 (2006)
PubMed id: 16964966  
 
 
X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcal surface protein PAM.
S.E.Cnudde, M.Prorok, F.J.Castellino, J.H.Geiger.
 
  ABSTRACT  
 
The crystal structure of the human Pg-derived angiogenesis inhibitor, angiostatin, complexed to VEK-30, a peptide from the group A streptococcal surface protein, PAM, was determined and refined to 2.3 A resolution. This is the first structure of angiostatin bound to a ligand and provides a model of the interaction between Pg and streptococcal-derived pathogenic proteins. VEK-30 contains a "through-space isostere" for C-terminal lysine, wherein Arg and Glu side chains, separated by one helical turn, bind within the bipolar angiostatin kringle 2 (K2) domain lysine-binding site. VEK-30 also makes several contacts with K2 residues that exist outside of the canonical LBS and are not conserved among the other Pg kringles, thus providing a molecular basis for the selectivity of VEK-30 for K2. The structure also shows that Pg kringle domains undergo significant structural rearrangement relative to one another and reveals dimerization between two molecules of angiostatin and VEK-30 related by crystallographic symmetry. This dimerization, which exists only in the crystal structure, is consistent with the parallel coiled-coil full-length PAM dimer expected from sequence similarities and homology modeling.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19800007 M.Wang, J.Zajicek, J.H.Geiger, M.Prorok, and F.J.Castellino (2010).
Solution structure of the complex of VEK-30 and plasminogen kringle 2.
  J Struct Biol, 169, 349-359.
PDB code: 2kj4
19473980 A.C.Tharp, M.Laha, P.Panizzi, M.W.Thompson, P.Fuentes-Prior, and P.E.Bock (2009).
Plasminogen Substrate Recognition by the Streptokinase-Plasminogen Catalytic Complex Is Facilitated by Arg253, Lys256, and Lys257 in the Streptokinase {beta}-Domain and Kringle 5 of the Substrate.
  J Biol Chem, 284, 19511-19521.  
18039665 Q.Fu, M.Figuera-Losada, V.A.Ploplis, S.Cnudde, J.H.Geiger, M.Prorok, and F.J.Castellino (2008).
The lack of binding of VEK-30, an internal peptide from the group A streptococcal M-like protein, PAM, to murine plasminogen is due to two amino acid replacements in the plasminogen kringle-2 domain.
  J Biol Chem, 283, 1580-1587.  
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 code is shown on the right.