3HOA | pdb_00003hoa

Crystal structure of the Thermus thermophilus M32 carboxypeptidase

• PDB DOI: https://doi.org/10.2210/pdb3HOA/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli
• Mutation(s): No 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.251 (Depositor) 
• R-Value Work: 
  0.218 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

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

• PubMed: 19544567 
• DOI: https://doi.org/10.1002/prot.22478
• Primary Citation 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.16 kDa 
• Atom Count: 8,689 
• Modeled Residue Count: 1,018 
• Deposited Residue Count: 1,018 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermostable carboxypeptidase 1	A, B	509	Thermus thermophilus HB27	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.251 (Depositor) 
• R-Value Work:  0.218 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.61	α = 90
b = 84.33	β = 93.75
c = 109.05	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description