1FBX | pdb_00001fbx

CRYSTAL STRUCTURE OF ZINC-CONTAINING E.COLI GTP CYCLOHYDROLASE I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.251 (Depositor) 
  • R-Value Work: 
    0.202 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1FBX

This is version 1.3 of the entry. See complete history

Literature

Zinc plays a key role in human and bacterial GTP cyclohydrolase I.

Auerbach, G.Herrmann, A.Bracher, A.Bader, G.Gutlich, M.Fischer, M.Neukamm, M.Garrido-Franco, M.Richardson, J.Nar, H.Huber, R.Bacher, A.

(2000) Proc Natl Acad Sci U S A 97: 13567-13572

  • DOI: https://doi.org/10.1073/pnas.240463497
  • Primary Citation Related Structures: 
    1FB1, 1FBX

  • PubMed Abstract: 

    The crystal structure of recombinant human GTP cyclohydrolase I was solved by Patterson search methods by using the coordinates of the Escherichia coli enzyme as a model. The human as well as bacterial enzyme were shown to contain an essential zinc ion coordinated to a His side chain and two thiol groups in each active site of the homodecameric enzymes that had escaped detection during earlier studies of the E. coli enzyme. The zinc ion is proposed to generate a hydroxyl nucleophile for attack of imidazole ring carbon atom eight of the substrate, GTP. It may also be involved in the hydrolytic release of formate from the intermediate, 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-triphosphate, and in the consecutive Amadori rearrangement of the ribosyl moiety.


  • Organizational Affiliation
    • Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 372.51 kDa 
  • Atom Count: 26,025 
  • Modeled Residue Count: 3,315 
  • Deposited Residue Count: 3,315 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTP CYCLOHYDROLASE I
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
221Escherichia coliMutation(s): 0 
EC: 3.5.4.16
UniProt
Find proteins for P0A6T5 (Escherichia coli (strain K12))
Explore P0A6T5 
Go to UniProtKB:  P0A6T5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6T5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
CA [auth G]
EA [auth H]
GA [auth I]
IA [auth J]
JA [auth K]
CA [auth G],
EA [auth H],
GA [auth I],
IA [auth J],
JA [auth K],
MA [auth L],
OA [auth M],
P [auth A],
QA [auth N],
S [auth B],
SA [auth O],
U [auth C],
W [auth D],
Y [auth E],
Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth F]
BA [auth G]
DA [auth H]
FA [auth I]
HA [auth J]
AA [auth F],
BA [auth G],
DA [auth H],
FA [auth I],
HA [auth J],
KA [auth K],
LA [auth L],
NA [auth M],
PA [auth N],
Q [auth A],
R [auth B],
RA [auth O],
T [auth C],
V [auth D],
X [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.251 (Depositor) 
  • R-Value Work:  0.202 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 227.69α = 90
b = 314.19β = 90
c = 132.57γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Derived calculations