1QQ9

STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH METHIONINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interactions of Streptomyces griseus aminopeptidase with a methionine product analogue: a structural study at 1.53 A resolution.

Gilboa, R.Greenblatt, H.M.Perach, M.Spungin-Bialik, A.Lessel, U.Wohlfahrt, G.Schomburg, D.Blumberg, S.Shoham, G.

(2000) Acta Crystallogr.,Sect.D 56: 551-558

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SGAP is an aminopeptidase present in the extracellular fluid of Streptomyces griseus cultures. It is a double-zinc enzyme with a strong preference for large hydrophobic amino-terminus residues. It is a monomeric (30 kDa) heat-stable enzyme, with a hi ...

    SGAP is an aminopeptidase present in the extracellular fluid of Streptomyces griseus cultures. It is a double-zinc enzyme with a strong preference for large hydrophobic amino-terminus residues. It is a monomeric (30 kDa) heat-stable enzyme, with a high and efficient catalytic activity modulated by calcium ions. The small size, high activity and heat stability make SGAP a very attractive enzyme for various biotechnological applications. Only one other related aminopeptidase (Aeromonas proteolytica AP; AAP) has been structurally analyzed to date and its structure was shown to be considerably similar to SGAP, despite the low sequence homology between the two enzymes. The motivation for the detailed structural analysis of SGAP originated from a strong mechanistic interest in the family of double-zinc aminopeptidases, combined with the high potential applicability of these enzymes. The 1.75 A crystallographic structure of native SGAP has been previously reported, but did not allow critical mechanistic interpretations owing to inconclusive structural regions around the active site. A more accurate structure of SGAP at 1.58 A resolution is reported in this paper, along with the 1.53 A resolution structure of the SGAP complex with inhibitory methionine, which is also a product of the SGAP catalytic process. These two high-resolution structures enable a better understanding of the SGAP binding mode of both substrates and products. These studies allowed the tracing of the previously disordered region of the enzyme (Glu196-Arg202) and the identification of some of the functional groups of the enzyme that are involved in enzyme-substrate interactions (Asp160, Met161, Gly201, Arg202 and Phe219). These studies also suggest that Glu131 is directly involved in the catalytic mechanism of SGAP, probably as the hydrolytic nucleophile. The structural results are compared with a recent structure of AAP with an hydroxamate inhibitor in order to draw general functional conclusions which are relevant for this family of low molecular-weight aminopeptidases.


    Related Citations: 
    • Streptomyces griseus aminopeptidase: X-ray crystallographic structure at 1.75 A resolution.
      Greenblatt, H.M.,Almog, O.,Maras, B.,Spungin-Bialik, A.,Barra, D.,Blumberg, S.,Shoham, G.
      (1997) J.Mol.Biol. 265: 620
    • Inhibition of Streptomyces griseus aminopeptidase and effects of calcium ions on catalysis and binding comparisons with the homologous enzyme Aeromonas proteolytica aminopeptidase.
      Papir, G.,Spungin-Bialik, A.,Ben-Meir, D.,Fudim, E.,Gilboa, R.,Greenblatt, H.M.,Shoham, G.,Lessel, U.,Schomburg, D.,Ashkenazi, R.,Blumberg, S.
      (1998) Eur.J.Biochem. 258: 313
    • Aminopeptidase from Streptomyces griseus: primary structure and comparison with other zinc-containing aminopeptidases.
      Maras, B.,Greenblatt, H.M.,Shoham, G.,Spungin-Bialik, A.,Blumberg, S.,Barra, D.
      (1996) Eur.J.Biochem. 236: 843


    Organizational Affiliation

    Department of Inorganic Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel. gil2@vms.huji.ac.il




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMINOPEPTIDASE
A
284Streptomyces griseus subsp. griseus (strain JCM 4626 / NBRC 13350)Mutation(s): 0 
EC: 3.4.11.24
Find proteins for P80561 (Streptomyces griseus subsp. griseus (strain JCM 4626 / NBRC 13350))
Go to UniProtKB:  P80561
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MET
Query on MET

Download SDF File 
Download CCD File 
A
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
METKi: 8700000 nM BINDINGMOAD
METKi: 8700000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.148 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.830α = 90.00
b = 61.830β = 90.00
c = 146.610γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance