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

PDB DOI: 10.2210/pdb2BC9/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.269
R-Value Work: 0.234
R-Value Observed: 0.241

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: 10.1038/nature04510
Primary Citation of Related Structures:
2B8W, 2B92, 2BC9, 2D4H

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.

Related Citations:

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

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

Organizational Affiliation:

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-induced guanylate-binding protein 1	A	328	Homo sapiens	Mutation(s): 0 Gene Names: GBP1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P32455 (Homo sapiens) Explore P32455 Go to UniProtKB: P32455
PHAROS: P32455
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32455
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction