Crystal structure of the Thermus thermophilus M32 carboxypeptidase

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.223 

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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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermostable carboxypeptidase 1
A, B
509Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1715
Find proteins for Q72GY3 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72GY3 
Go to UniProtKB:  Q72GY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72GY3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • 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
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

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