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 
  • R-Value Observed: 0.152 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1111/febs.13210
  • Primary Citation of Related Structures:  
    3V7Z, 4DUK

  • 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 1.57 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase T326Thermoactinomyces vulgarisMutation(s): 0 
Gene Names: cpt
EC: 3.4.17.18
UniProt
Find proteins for P29068 (Thermoactinomyces vulgaris)
Explore P29068 
Go to UniProtKB:  P29068
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29068
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BZS
Query on BZS

Download Ideal Coordinates CCD File 
F [auth A]L-BENZYLSUCCINIC ACID
C11 H12 O4
GTOFKXZQQDSVFH-SECBINFHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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AA [auth A]
DA [auth A]
EA [auth A]
FA [auth A]
GA [auth A]
AA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth A],
C [auth A],
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.939α = 90
b = 157.939β = 90
c = 104.437γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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