3HOA

Crystal structure of the Thermus thermophilus M32 carboxypeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insight into the substrate length restriction of M32 carboxypeptidases: Characterization of two distinct subfamilies.

Lee, M.M.Isaza, C.E.White, J.D.Chen, R.P.Liang, G.F.He, H.T.Chan, S.I.Chan, M.K.

(2009) Proteins 77: 647-657

  • DOI: 10.1002/prot.22478
  • Primary Citation of Related Structures:  
    3HOA, 3HQ2

  • PubMed Abstract: 
  • M32 carboxypeptidases are a distinct family of HEXXH metalloproteases whose structures exhibit a narrow substrate groove that is blocked at one end. Structural alignments with other HEXXH metalloprotease-peptide complexes suggested an orientation in which the substrate is directed towards the back of the groove ...

    M32 carboxypeptidases are a distinct family of HEXXH metalloproteases whose structures exhibit a narrow substrate groove that is blocked at one end. Structural alignments with other HEXXH metalloprotease-peptide complexes suggested an orientation in which the substrate is directed towards the back of the groove. This led us to hypothesize, and subsequently confirm that the maximum substrate length for M32 carboxypeptidases is restricted. Structural and sequence analyses implicate a highly conserved Arg at the back of the groove as being critical for this length restriction. However, the Thermus thermophilus and Bacillus subtilis M32 members lack this conserved Arg. Herein, we present the biochemical and structural characterization of these two proteins. Our findings support the important role of the conserved Arg in maintaining the length restriction, and reveal a proline-rich loop as an alternate blocking strategy. Based on our results, we propose that M32 carboxypeptidases from Bacilli belong to a separate subfamily.


    Organizational Affiliation

    The Ohio State Biophysics Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thermostable carboxypeptidase 1A, B509Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1715
EC: 3.4.17.19
UniProt
Find proteins for Q72GY3 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72GY3 
Go to UniProtKB:  Q72GY3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.61α = 90
b = 84.33β = 93.75
c = 109.05γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2009-06-01 
  • Released Date: 2009-06-30 
  • Deposition Author(s): Lee, M.M., Chan, M.K.

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2021-03-31
    Changes: Data collection, Derived calculations