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PDBsum entry 1ao5

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protein ligands Protein-protein interface(s) links
Serine protease PDB id
1ao5
Jmol
Contents
Protein chains
236 a.a. *
Ligands
NAG-NAG ×2
Waters ×119
* Residue conservation analysis
PDB id:
1ao5
Name: Serine protease
Title: Mouse glandular kallikrein-13 (prorenin converting enzyme)
Structure: Glandular kallikrein-13. Chain: a, b. Synonym: prorenin converting enzyme (prece), epidermal grow binding protein type b (egf-bp b). Ec: 3.4.21.35
Source: Mus musculus. House mouse. Organism_taxid: 10090. Strain: swiss webster. Organ: submandibular gland
Biol. unit: Tetramer (from PQS)
Resolution:
2.60Å     R-factor:   0.197     R-free:   0.271
Authors: D.E.Timm
Key ref:
D.E.Timm (1997). The crystal structure of the mouse glandular kallikrein-13 (prorenin converting enzyme). Protein Sci, 6, 1418-1425. PubMed id: 9232643 DOI: 10.1002/pro.5560060706
Date:
16-Jul-97     Release date:   15-Oct-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P36368  (EGFB2_MOUSE) -  Epidermal growth factor-binding protein type B
Seq:
Struc:
261 a.a.
236 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.119  - Kallikrein 13.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   1 term 
  Biological process     proteolysis   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1002/pro.5560060706 Protein Sci 6:1418-1425 (1997)
PubMed id: 9232643  
 
 
The crystal structure of the mouse glandular kallikrein-13 (prorenin converting enzyme).
D.E.Timm.
 
  ABSTRACT  
 
A crystal structure of the serine protease, mouse glandular kallikrein 13 (mGK-13) has been determined at 2.6-A resolution. This enzyme, isolated from the mouse submandibular gland, is also known as prorenin-converting enzyme and cleaves submandibular gland Ren-2 prorenin to yield active renin. The mGK-13 structure is similar to other members of the mammalian serine protease family, having five conserved disulfide bonds and an active site located in the cleft between two beta-barrel domains. The mGK-13 structure reveals for the first time an ordered kallikrein loop conformation containing a short 3(10) helix. This loop is disordered in the related porcine pancreatic kallikrein and rat submandibular tonin structures. The kallikrein loop is in close spatial proximity to the active site and is also involved in a dimeric arrangement of mGK-13. The catalytic specificity of mGK-13 for Ren-2 prorenin was studied by modeling a prorenin-derived peptide into the active site of mGK-13. This model emphasizes two electronegative substrate specificity pockets on the mGK-13 surface, which could accommodate the dibasic P2 and P1 residues at the site of prorenin cleavage by mGK-13.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Electron density. section f the refined 2F0 - F, density map is presented in the of the kallikrein loop residues Leu and Leu 95D at the bottom and 57 t the upper left. The section is con- toured at a level of 1.3 sigma.
Figure 3.
Fig. 3. Peptide modeledin the mGK13 active site. A modeledhexamericpeptidefromRen-2proreninis represented in (A) a space-filling electrostatic surface diagram calculated usingGRASP (Nicholls et al., 1991) and (B) a schematic orm.Positiveand negative electrostatic surface potentials are displayed in blue andred,respectively. The GK-3 substrate biningpocket, S3, ould accommodate polar orhydrophobic residues; 2 accommodates thebasic 2 lysine interacting withAsp102and Ser 214; S1 accommodates thebasicP1 arginine interactingwithAsp189; P' 1 and coudaccommodatesmallpolar or hydrophobic residues; accommodates hydrophobic residues. Thekallikreinloopislabeled KL.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1997, 6, 1418-1425) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20615447 P.Goettig, V.Magdolen, and H.Brandstetter (2010).
Natural and synthetic inhibitors of kallikrein-related peptidases (KLKs).
  Biochimie, 92, 1546-1567.  
19846563 W.Niu, Z.Chen, L.A.Bush-Pelc, A.Bah, P.S.Gandhi, and E.Di Cera (2009).
Mutant N143P reveals how Na+ activates thrombin.
  J Biol Chem, 284, 36175-36185.
PDB codes: 3jz1 3jz2
18186617 A.E.Schmidt, M.F.Sun, T.Ogawa, S.P.Bajaj, and D.Gailani (2008).
Functional role of residue 193 (chymotrypsin numbering) in serine proteases: influence of side chain length and beta-branching on the catalytic activity of blood coagulation factor XIa.
  Biochemistry, 47, 1326-1335.  
18844454 J.A.Clements (2008).
Reflections on the tissue kallikrein and kallikrein-related peptidase family - from mice to men - what have we learnt in the last two decades?
  Biol Chem, 389, 1447-1454.  
15651049 G.Laxmikanthan, S.I.Blaber, M.J.Bernett, I.A.Scarisbrick, M.A.Juliano, and M.Blaber (2005).
1.70 A X-ray structure of human apo kallikrein 1: structural changes upon peptide inhibitor/substrate binding.
  Proteins, 58, 802-814.
PDB code: 1spj
15456490 A.Zivelin, T.Ogawa, S.Bulvik, M.Landau, J.R.Toomey, J.Lane, U.Seligsohn, and D.Gailani (2004).
Severe factor XI deficiency caused by a Gly555 to Glu mutation (factor XI-Glu555): a cross-reactive material positive variant defective in factor IX activation.
  J Thromb Haemost, 2, 1782-1789.  
11863437 M.C.Hsieh, and B.S.Cooperman (2002).
Inhibition of prostate-specific antigen (PSA) by alpha(1)-antichymotrypsin: salt-dependent activation mediated by a conformational change.
  Biochemistry, 41, 2990-2997.  
11468412 A.L.Carvalho, J.M.Dias, L.Sanz, A.Romero, J.J.Calvete, and M.J.Romão (2001).
Purification, crystallization and identification by X-ray analysis of a prostate kallikrein from horse seminal plasma.
  Acta Crystallogr D Biol Crystallogr, 57, 1180-1183.  
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.