3GMT

Crystal structure of adenylate kinase from burkholderia pseudomallei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state.

Buchko, G.W.Robinson, H.Abendroth, J.Staker, B.L.Myler, P.J.

(2010) Biochem.Biophys.Res.Commun. 394: 1012-1017

  • DOI: 10.1016/j.bbrc.2010.03.112

  • PubMed Abstract: 
  • In all organisms adenylate kinases (Adks) play a vital role in cellular energy metabolism and nucleic acid synthesis. Due to differences in catalytic properties between the Adks found in prokaryotes and in the cytoplasm of eukaryotes, there is intere ...

    In all organisms adenylate kinases (Adks) play a vital role in cellular energy metabolism and nucleic acid synthesis. Due to differences in catalytic properties between the Adks found in prokaryotes and in the cytoplasm of eukaryotes, there is interest in targeting this enzyme for new drug therapies against infectious bacterial agents. Here we report the 2.1A resolution crystal structure for the 220-residue Adk from Burkholderia pseudomallei (BpAdk), the etiological agent responsible for the infectious disease melioidosis. The general structure of apo BpAdk is similar to other Adk structures, composed of a CORE subdomain with peripheral ATP-binding (ATP(bd)) and LID subdomains. The two molecules in the asymmetric unit have significantly different conformations, with a backbone RMSD of 1.46 A. These two BpAdk conformations may represent 'open' Adk sub-states along the preferential pathway to the 'closed' substrate-bound state.


    Related Citations: 
    • Combining functional and structural genomics to sample the essential Burkholderia structome.
      Baugh, L.,Gallagher, L.A.,Patrapuvich, R.,Clifton, M.C.,Gardberg, A.S.,Edwards, T.E.,Armour, B.,Begley, D.W.,Dieterich, S.H.,Dranow, D.M.,Abendroth, J.,Fairman, J.W.,Fox, D.,Staker, B.L.,Phan, I.,Gillespie, A.,Choi, R.,Nakazawa-Hewitt, S.,Nguyen, M.T.,Napuli, A.,Barrett, L.,Buchko, G.W.,Stacy, R.,Myler, P.J.,Stewart, L.J.,Manoil, C.,Van Voorhis, W.C.
      (2013) Plos One 8: e53851


    Organizational Affiliation

    Biological Sciences Division and Seattle Structural Genomics Center for Infectious Disease, Pacific Northwest National Laboratory, Richland, WA 99352, USA. garry.buchko@pnl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylate kinase
A, B
230Burkholderia pseudomallei (strain 1710b)Mutation(s): 0 
Gene Names: adk
EC: 2.7.4.3
Find proteins for Q3JVB1 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JVB1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 62.230α = 90.00
b = 66.000β = 113.69
c = 63.760γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
PARROTphasing
XDSdata reduction
ARP/wARPmodel building
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-10-30
    Type: Database references