Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 44.93 kDa 
• Atom Count: 2822 
• Residue Count: 343 
• Unique protein chains: 1

2BZ0

Crystal Structure of E. coli GTP cyclohydrolase II in complex with GTP analogue, GMPcPP, and Zinc

• DOI: 10.2210/pdb2BZ0/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-08-09 Released: 2005-08-19 
• Deposition Author(s): Ren, J., Kotaka, M., Lockyer, M., Lamb, H.K., Hawkins, A.R., Stammers, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

GTP Cyclohydrolase II Structure and Mechanism.

Ren, J., Kotaka, M., Lockyer, M., Lamb, H.K., Hawkins, A.R., Stammers, D.K.

(2005) J Biol Chem 280: 36912

• PubMed: 16115872 
• DOI: 10.1074/jbc.M507725200
• Primary Citation of Related Structures:  
  2BZ1, 2BZ0


• PubMed Abstract: 
  

GTP cyclohydrolase II converts GTP to 2,5-diamino-6-beta-ribosyl-4(3H)-pyrimidinone 5'-phosphate, formate and pyrophosphate, the first step in riboflavin biosynthesis. The essential role of riboflavin in metabolism and the absence of GTP cyclohydrolase II in higher eukaryotes makes it a potential novel selective antimicrobial drug target. GTP cyclohydrolase II catalyzes a distinctive overall reaction from GTP cyclohydrolase I; the latter converts GTP to dihydroneopterin triphosphate, utilized in folate and tetrahydrobiopterin biosynthesis. The structure of GTP cyclohydrolase II determined at 1.54-A resolution reveals both a different protein fold to GTP cyclohydrolase I and distinctive molecular recognition determinants for GTP; although in both enzymes there is a bound catalytic zinc. The GTP cyclohydrolase II.GMPCPP complex structure shows Arg(128) interacting with the alpha-phosphonate, and thus in the case of GTP, Arg(128) is positioned to act as the nucleophile for pyrophosphate release and formation of the proposed covalent guanylyl-GTP cyclohydrolase II intermediate. Tyr(105) is identified as playing a key role in GTP ring opening; it is hydrogen-bonded to the zinc-activated water molecule, the latter being positioned for nucleophilic attack on the guanine C-8 atom. Although GTP cyclohydrolase I and GTP cyclohydrolase II both use a zinc ion for the GTP ring opening and formate release, different residues are utilized in each case to catalyze this reaction step.

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Organizational Affiliation: 

Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP CYCLOHYDROLASE II	A, B	196	Escherichia coli	Mutation(s): 0  EC: 3.5.4.25
Find proteins for P0A7I7 (Escherichia coli (strain K12)) Explore P0A7I7  Go to UniProtKB:  P0A7I7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G2P	A, B	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C11 H18 N5 O13 P3 GXTIEXDFEKYVGY-KQYNXXCUSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.08	α = 90
b = 99.08	β = 90
c = 96.29	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-09 
• Released Date: 2005-08-19 
Deposition Author(s): Ren, J., Kotaka, M., Lockyer, M., Lamb, H.K., Hawkins, A.R., Stammers, D.K.

Revision History 

• Version 1.0: 2005-08-19
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance