4DUK

Carboxypeptidase T with L-BENZYLSUCCINIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the broad substrate specificity of carboxypeptidase T from Thermoactinomyces vulgaris.

Akparov, V.K.h.Timofeev, V.I.Khaliullin, I.G.Svedas, V.Chestukhina, G.G.Kuranova, I.P.

(2015) Febs J. 282: 1214-1224

  • DOI: 10.1111/febs.13210
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of carboxypeptidase T (CpT) complexes with phenylalanine and arginine substrate analogs - benzylsuccinic acid and (2-guanidinoethylmercapto)succinic acid - were determined by the molecular replacement method at resolutions of 1 ...

    The crystal structures of carboxypeptidase T (CpT) complexes with phenylalanine and arginine substrate analogs - benzylsuccinic acid and (2-guanidinoethylmercapto)succinic acid - were determined by the molecular replacement method at resolutions of 1.57 Å and 1.62 Å to clarify the broad substrate specificity profile of the enzyme. The conservative Leu211 and Leu254 residues (also present in both carboxypeptidase A and carboxypeptidase B) were shown to be structural determinants for recognition of hydrophobic substrates, whereas Asp263 was for recognition of positively charged substrates. Mutations of these determinants modify the substrate profile: the CpT variant Leu211Gln acquires carboxypeptidase B-like properties, and the CpT variant Asp263Asn the carboxypeptidase A-like selectivity. The Pro248-Asp258 loop interacting with Leu254 and Tyr255 was shown to be responsible for recognition of the substrate's C-terminal residue. Substrate binding at the S1' subsite leads to the ligand-dependent shift of this loop, and Leu254 side chain movement induces the conformation rearrangement of the Glu277 residue crucial for catalysis. This is a novel insight into the substrate selectivity of metallocarboxypeptidases that demonstrates the importance of interactions between the S1' subsite and the catalytic center.


    Organizational Affiliation

    State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase T
A
326Thermoactinomyces vulgarisGene Names: cpt
EC: 3.4.17.18
Find proteins for P29068 (Thermoactinomyces vulgaris)
Go to UniProtKB:  P29068
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BZS
Query on BZS

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A
L-BENZYLSUCCINIC ACID
C11 H12 O4
GTOFKXZQQDSVFH-SECBINFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.151 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 157.939α = 90.00
b = 157.939β = 90.00
c = 104.437γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
REFMACrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references