6K63

The crystal structure of cytidine deaminase from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Biochemical and structural analysis of the Klebsiella pneumoniae cytidine deaminase CDA.

Liu, W.Shang, F.Chen, Y.Lan, J.Wang, L.Chen, J.Gao, P.Ha, N.C.Quan, C.Nam, K.H.Xu, Y.

(2019) Biochem Biophys Res Commun 519: 280-286

  • DOI: https://doi.org/10.1016/j.bbrc.2019.08.167
  • Primary Citation of Related Structures:  
    6K63

  • PubMed Abstract: 

    The emergence of drug-resistant strains of Klebsiella pneumoniae, has exacerbated the treatment and control of the disease caused by this bacterium. Cytidine deaminases (CDA) are zinc-dependent enzymes involved in the pyrimidine salvage pathway and catalyze the formation of uridine and deoxyuridine from cytidine and deoxycytidine, respectively. To illustrate the structural basis of CDA for a deeper knowledge of the molecular mechanisms underlying the salvage pathway, we reported here the biochemical and structural analysis of CDA from pathogenic K. pneumonia. KpCDA showed deaminase activity against cytidine as well as its analog cytarabine. The deaminase activity of KpCDA on cytarabine was 1.8 times higher than that on cytidine. KpCDA is composed of an N-terminal catalytic domain and a C-terminal noncatalytic domain. Zinc, which is involved in the activity of the catalytic domain, is coordinated by His102, Cys129, and Cys132, and two 1,4-dioxane molecules were present at the active sites. KpCDA exists as a dimer and shows distinct dimeric interface compared with other CDAs. Our results provide the structural features of KpCDA, and KpCDA might be a potential antibacterial target for the disease caused by K. pneumoniae.


  • Organizational Affiliation

    Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China. Electronic address: mikyeken@dlnu.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytidine deaminase
A, B, C, D
294Klebsiella pneumoniae subsp. pneumoniae MGH 78578Mutation(s): 0 
Gene Names: cdd
EC: 3.5.4.5
UniProt
Find proteins for A6TBN1 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TBN1 
Go to UniProtKB:  A6TBN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6TBN1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DIO
Query on DIO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D],
R [auth D],
S [auth D]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
O [auth C],
T [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.748α = 90
b = 151.748β = 90
c = 120.155γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31200556
National Natural Science Foundation of ChinaChina21272031

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description