1KUH

ZINC PROTEASE FROM STREPTOMYCES CAESPITOSUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the zinc endoprotease from Streptomyces caespitosus.

Kurisu, G.Kinoshita, T.Sugimoto, A.Nagara, A.Kai, Y.Kasai, N.Harada, S.

(1997) J Biochem 121: 304-308

  • DOI: 10.1093/oxfordjournals.jbchem.a021587
  • Primary Citation of Related Structures:  
    1KUH

  • PubMed Abstract: 
  • A zinc endoprotease produced by Streptomyces caespitosus (ScNP) specifically hydrolyzes the peptide bond at the imino side of aromatic residues and is the smallest protease found to date. Although ScNP carries the zinc-binding sequence HEXXH, its primary structure of 132 amino acid residues differs from those of other known zinc metalloendoproteases ...

    A zinc endoprotease produced by Streptomyces caespitosus (ScNP) specifically hydrolyzes the peptide bond at the imino side of aromatic residues and is the smallest protease found to date. Although ScNP carries the zinc-binding sequence HEXXH, its primary structure of 132 amino acid residues differs from those of other known zinc metalloendoproteases. X-ray structural analysis of ScNP at 1.6 A resolution revealed that despite a lack of sequence homology, the common topological feature of main-chain folding and a beta-turn containing methionine, which is a feature of the zinc metalloendoprotease superfamily of metzincins, is conserved in ScNP. The zinc atom of ScNP is tetrahedrally ligated by the two histidines in the HEXXH sequence, an aspartate residue and a water molecule. Thus, ScNP represents a novel subfamily of metzincins with a HEXXHXXGXXD zinc-binding sequence. A plausible substrate recognition pocket to which aromatic residues bind is located near the catalytic zinc ion.


    Related Citations: 
    • Complete Amino Acid Sequence of a Zinc Metalloendoprotease from Streptomyces Caespitosus
      Harada, S., Kinoshita, T., Kasai, N., Tsunasawa, S., Sakiyama, F.
      (1995) Eur J Biochem 233: 683
    • Crystallization and Main-Chain Structure of Neutral Protease from Streptomyces Caespitosus
      Harada, S., Kitadokoro, K., Kinoshita, T., Kai, Y., Kasai, N.
      (1991) J Biochem 110: 46

    Organizational Affiliation

    Department of Applied Chemistry, Faculty of Engineering, Osaka University. genji@ap.chem.eng.osaka-u.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ZINC PROTEASEA132Streptomyces caespitosusMutation(s): 0 
Gene Names: snpA
EC: 3.4.24.77
UniProt
Find proteins for P56406 (Streptomyces caespitosus)
Explore P56406 
Go to UniProtKB:  P56406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56406
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.21α = 90
b = 55.27β = 90
c = 37.6γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance