Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.88 kDa 
• Atom Count: 3035 
• Residue Count: 358 
• Unique protein chains: 1

2R7K

Crystal structure of FAICAR synthetase (PurP) from M. jannaschii complexed with AMPPCP and AICAR

• DOI: 10.2210/pdb2R7K/pdb

• Classification: LIGASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-09 Released: 2007-12-04 
• Deposition Author(s): Zhang, Y., White, R.H., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

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

• PubMed: 18069798 
• DOI: 10.1021/bi701406g
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase	A	361	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: purP EC: 6.3.4 (PDB Primary Data), 6.3.4.23 (UniProt)
Find proteins for Q57600 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Go to UniProtKB:  Q57600

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP	A	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
AMZ	A	AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE C9 H15 N4 O8 P NOTGFIUVDGNKRI-UUOKFMHZSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.435	α = 90
b = 109.435	β = 90
c = 255.994	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-09-09 
• Released Date: 2007-12-04 
Deposition Author(s): Zhang, Y., White, R.H., Ealick, S.E.

Revision History 

• 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