Crystal structure of PurP from Pyrococcus furiosus complexed with ADP

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii.

Zhang, Y.White, R.H.Ealick, S.E.

(2008) Biochemistry 47: 205-217

  • DOI: https://doi.org/10.1021/bi701406g
  • Primary Citation of Related Structures:  
    2R7K, 2R7L, 2R7M, 2R7N, 2R84, 2R85, 2R86, 2R87

  • PubMed Abstract: 

    Purine biosynthesis requires 10 enzymatic steps in higher organisms, while prokaryotes require an additional enzyme for step 6. In most organisms steps 9 and 10 are catalyzed by the purH gene product, a bifunctional enzyme with both 5-formaminoimidazole-4-carboxamide ribonucleotide (FAICAR) synthase and inosine monophosphate (IMP) cyclohydrolase activity. Recently it was discovered that Archaea utilize different enzymes to catalyze steps 9 and 10. An ATP-dependent FAICAR synthetase is encoded by the purP gene, and IMP cyclohydrolase is encoded by the purO gene. We have determined the X-ray crystal structures of FAICAR synthetase from Methanocaldococcus jannaschii complexed with various ligands, including the tertiary substrate complex and product complex. The enzyme belongs to the ATP grasp superfamily and is predicted to use a formyl phosphate intermediate formed by an ATP-dependent phosphorylation. In addition, we have determined the structures of a PurP orthologue from Pyrococcus furiosus, which is functionally unclassified, in three crystal forms. With approximately 50% sequence identity, P. furiosus PurP is structurally homologous to M. jannaschii PurP. A phylogenetic analysis was performed to explore the possible role of this functionally unclassified PurP.

  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PurP protein PF1517
A, B, C, D, E
A, B, C, D, E, F
334Pyrococcus furiosusMutation(s): 0 
Find proteins for Q8U0R7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U0R7 
Go to UniProtKB:  Q8U0R7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U0R7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
J [auth A]
N [auth B]
S [auth C]
AA [auth E],
EA [auth F],
J [auth A],
N [auth B],
S [auth C],
W [auth D]
C10 H15 N5 O10 P2
Query on PO4

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth F]
DA [auth F]
G [auth A]
H [auth A]
BA [auth F],
CA [auth F],
DA [auth F],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
T [auth D],
U [auth D],
V [auth D],
X [auth E],
Y [auth E],
Z [auth E]
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.095α = 90
b = 127.222β = 102.85
c = 121.673γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
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: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description