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PDBsum entry 1qrz

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protein Protein-protein interface(s) links
Hydrolase PDB id
1qrz
Jmol
Contents
Protein chain
246 a.a. *
Waters ×509
* Residue conservation analysis
PDB id:
1qrz
Name: Hydrolase
Title: Catalytic domain of plasminogen
Structure: Plasminogen. Chain: a, b, c, d. Fragment: catalytic domain. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606.
Resolution:
2.00Å     R-factor:   0.235     R-free:   0.294
Authors: E.Peisach,J.Wang,T.De Los Santos,E.Reich,D.Ringe
Key ref:
E.Peisach et al. (1999). Crystal structure of the proenzyme domain of plasminogen. Biochemistry, 38, 11180-11188. PubMed id: 10460175 DOI: 10.1021/bi991130r
Date:
16-Jun-99     Release date:   14-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00747  (PLMN_HUMAN) -  Plasminogen
Seq:
Struc:
 
Seq:
Struc:
810 a.a.
246 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: 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     proteolysis   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1021/bi991130r Biochemistry 38:11180-11188 (1999)
PubMed id: 10460175  
 
 
Crystal structure of the proenzyme domain of plasminogen.
E.Peisach, J.Wang, T.de los Santos, E.Reich, D.Ringe.
 
  ABSTRACT  
 
We have solved the X-ray crystal structure of the proenzyme form of the catalytic domain of plasminogen, with the nonessential mutations M585Q, V673M, and M788L, to 2.0 A resolution. The structure presents an inactive protease characterized by Asp740 (chymotrypsinogen 194) hydrogen bonded to His586 (chymotrypsinogen 40), preventing proper formation of the oxyanion hole and S1 specificity pocket. In addition, the catalytic triad residues are misplaced relative to the active conformation adopted by serine proteases in the chymotrypsin family. Finally, a unique form of zymogen inactivation is observed, characterized by a "foot-in-mouth" mechanism in which Trp761 (chymotrypsinogen 215) is folded into the S1 specificity pocket preventing substrate binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17996400 P.K.Shah, L.P.Tripathi, L.J.Jensen, M.Gahnim, C.Mason, E.E.Furlong, V.Rodrigues, K.P.White, P.Bork, and R.Sowdhamini (2008).
Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families.
  Gene, 407, 199-215.  
16279944 F.Carafoli, D.Y.Chirgadze, T.L.Blundell, and E.Gherardi (2005).
Crystal structure of the beta-chain of human hepatocyte growth factor-like/macrophage stimulating protein.
  FEBS J, 272, 5799-5807.
PDB code: 2asu
15211511 S.Terzyan, N.Wakeham, P.Zhai, K.Rodgers, and X.C.Zhang (2004).
Characterization of Lys-698-to-Met substitution in human plasminogen catalytic domain.
  Proteins, 56, 277-284.
PDB code: 1rjx
12080056 R.B.Turner, L.Liu, I.Y.Sazonova, and G.L.Reed (2002).
Structural elements that govern the substrate specificity of the clot-dissolving enzyme plasmin.
  J Biol Chem, 277, 33068-33074.  
11470437 C.Eigenbrot, D.Kirchhofer, M.S.Dennis, L.Santell, R.A.Lazarus, J.Stamos, and M.H.Ultsch (2001).
The factor VII zymogen structure reveals reregistration of beta strands during activation.
  Structure, 9, 627-636.
PDB code: 1jbu
11742690 K.Lähteenmäki, P.Kuusela, and T.K.Korhonen (2001).
Bacterial plasminogen activators and receptors.
  FEMS Microbiol Rev, 25, 531-552.  
11168406 R.Egelund, T.E.Petersen, and P.A.Andreasen (2001).
A serpin-induced extensive proteolytic susceptibility of urokinase-type plasminogen activator implicates distortion of the proteinase substrate-binding pocket and oxyanion hole in the serpin inhibitory mechanism.
  Eur J Biochem, 268, 673-685.  
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.