4DLK

Crystal Structure of ATP-Ca++ complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis.

Tuntland, M.L.Santarsiero, B.D.Johnson, M.E.Fung, L.W.

(2014) Acta Crystallogr.,Sect.D 70: 3057-3065

  • DOI: 10.1107/S1399004714021166
  • Primary Citation of Related Structures:  3QFF, 3R5H, 3V4S

  • PubMed Abstract: 
  • Structures of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis with various combinations of ATP, ADP, Mg(2+), bicarbonate and aminoimidazole ribonucleotide (AIR) in the active site are presented. The binding site of ...

    Structures of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis with various combinations of ATP, ADP, Mg(2+), bicarbonate and aminoimidazole ribonucleotide (AIR) in the active site are presented. The binding site of bicarbonate has only been speculated upon previously, but is shown here for the first time. The binding involves interactions with the conserved residues Arg272, His274 and Lys348. These structures provide insights into each ligand in the active site and allow a possible mechanism to be proposed for the reaction that converts bicarbonate and AIR, in the presence of ATP, to produce (N(5))-carboxyaminoimidazole ribonucleotide. The formation of a carboxyphosphate intermediate through ATP phosphoryl transfer is proposed, followed by carboxylation of AIR to give the product, facilitated by a cluster of conserved residues and an active-site water network.


    Organizational Affiliation

    Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoribosylaminoimidazole carboxylase, ATPase subunit
A, B
380Bacillus anthracisGene Names: purK
EC: 6.3.4.18
Find proteins for Q81ZH7 (Bacillus anthracis)
Go to UniProtKB:  Q81ZH7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.368α = 90.00
b = 84.476β = 90.00
c = 167.269γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Database references