Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37624.95 
• Atom Count: 2364 
• Residue Count: 328 
• Unique protein chains: 1

2BC9

Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with non-hydrolysable GTP analogue GppNHp

• DOI: 10.2210/pdb2BC9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2005-10-19 Released: 2006-03-07 
• Deposition Author(s): Ghosh, A., Praefcke, G.J.K., Renault, L., Wittinghofer, A., Herrmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.269 
• R-Value Work: 0.234 

Literature

How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP.

Ghosh, A., Praefcke, G.J., Renault, L., Wittinghofer, A., Herrmann, C.

(2006) Nature 440: 101-104

• PubMed: 16511497 
• DOI: 10.1038/nature04510
• Primary Citation of Related Structures:  
  2D4H, 2B92, 2B8W


• PubMed Abstract: 
  

Interferons are immunomodulatory cytokines that mediate anti-pathogenic and anti-proliferative effects in cells. Interferon-gamma-inducible human guanylate binding protein 1 (hGBP1) belongs to the family of dynamin-related large GTP-binding proteins, which share biochemical properties not found in other families of GTP-binding proteins such as nucleotide-dependent oligomerization and fast cooperative GTPase activity. hGBP1 has an additional property by which it hydrolyses GTP to GMP in two consecutive cleavage reactions. Here we show that the isolated amino-terminal G domain of hGBP1 retains the main enzymatic properties of the full-length protein and can cleave GDP directly. Crystal structures of the N-terminal G domain trapped at successive steps along the reaction pathway and biochemical data reveal the molecular basis for nucleotide-dependent homodimerization and cleavage of GTP. Similar to effector binding in other GTP-binding proteins, homodimerization is regulated by structural changes in the switch regions. Homodimerization generates a conformation in which an arginine finger and a serine are oriented for efficient catalysis. Positioning of the substrate for the second hydrolysis step is achieved by a change in nucleotide conformation at the ribose that keeps the guanine base interactions intact and positions the beta-phosphates in the gamma-phosphate-binding site.

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Related Citations: 

• Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins.
  Prakash, B.,Praefcke, G.J.,Renault, L.,Herrmann, C.,Wittinghofer, A.
  (2000) Nature 403: 567
• Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism.
  Prakash, B.,Renault, L.,Praefcke, G.J.,Herrmann, C.,Wittinghofer, A.
  (2000) Embo J. 19: 4555




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Organizational Affiliation: 

Abteilung Strukturelle Biologie, Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Interferon-induced guanylate-binding protein 1	A	328	Homo sapiens	Mutation(s): 0  Gene Names: GBP1 EC: 3.6.5.-
Find proteins for P32455 (Homo sapiens) Go to Gene View: GBP1 Go to UniProtKB:  P32455

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
GNP	A	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.269 
• R-Value Work: 0.234 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 54.884	α = 90.00
b = 101.104	β = 90.00
c = 149.261	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-19 
• Released Date: 2006-03-07 
• Deposition Author(s): Ghosh, A., Praefcke, G.J.K., Renault, L., Wittinghofer, A., Herrmann, C.

Revision History 

• Version 1.0: 2006-03-07
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-01-24
  Type: Structure summary