5X9Q

Crystal structure of HldC from Burkholderia pseudomallei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of D-glycero-Beta-D-manno-heptose-1-phosphate adenylyltransferase from Burkholderia pseudomallei.

Park, J.Kim, H.Kim, S.Lee, D.Kim, M.S.Shin, D.H.

(2018) Proteins 86: 124-131

  • DOI: https://doi.org/10.1002/prot.25398
  • Primary Citation of Related Structures:  
    5X9Q

  • PubMed Abstract: 

    The crystal structure of HldC from B. pseudomallei (BpHldC), the fourth enzyme of the heptose biosynthesis pathway, has been determined. BpHldC converts ATP and d-glycero-β-d-manno-heptose-1-phosphate into ADP-d-glycero-β-d-manno-heptose and pyrophosphate. The crystal structure of BpHldC belongs to the nucleotidyltransferase α/β phosphodiesterase superfamily sharing a common Rossmann-like α/β fold with a conserved T/HXGH sequence motif. The invariant catalytic key residues of BpHldC indicate that the core catalytic mechanism of BpHldC may be similar to that of other closest homologues. Intriguingly, a reorientation of the C-terminal helix seems to guide open and close states of the active site for the catalytic reaction.


  • Organizational Affiliation

    College of Pharmacy, Ewha W. University, Seoul, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative cytidylyltransferase
A, B, C, D
173Burkholderia pseudomallei K96243Mutation(s): 0 
Gene Names: BPSL0395
UniProt
Find proteins for Q63XZ4 (Burkholderia pseudomallei (strain K96243))
Explore Q63XZ4 
Go to UniProtKB:  Q63XZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63XZ4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.89α = 90
b = 119.37β = 110.81
c = 76.703γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic Of2015R1D1A1A01058942

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references