PDBsum entry 2d4h

Signaling protein

PDB id: 2d4h

Contents

Protein chains

299 a.a. *

284 a.a. *

Ligands

5GP ×2

Waters ×119

* Residue conservation analysis

PDB id:

2d4h

Name:

Signaling protein

Title:

Crystal-structure of the n-terminal large gtpase domain of human guanylate binding protein 1 (hgbp1) in complex with gmp

Structure:

Interferon-induced guanylate-binding protein 1. Chain: a, b. Fragment: n-terminal large gtpase domain. Synonym: gtp-binding protein 1, guanine nucleotide-binding protein 1, hugbp-1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: gbp1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.90Å R-factor: 0.235 R-free: 0.275

Authors:

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

Key ref:

A.Ghosh et al. (2006). How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP. Nature, 440, 101-104. PubMed id: 16511497 DOI: 10.1038/nature04510

Date:

19-Oct-05 Release date: 07-Mar-06

Protein chain

P32455  (GBP1_HUMAN) -  Guanylate-binding protein 1 from Homo sapiens

Seq: 592 a.a.

Struc: 299 a.a.

Protein chain

P32455  (GBP1_HUMAN) -  Guanylate-binding protein 1 from Homo sapiens

Seq: 592 a.a.

Struc: 284 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.3.6.1.- - ?????
• Enzyme class 3: Chains A, B: E.C.3.6.5.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1038/nature04510

Nature 440:101-104 (2006)

PubMed id: 16511497

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

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

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.

Selected figure(s)

Figure 2.
Figure 2: Structural analysis of the GTPase reaction. a, Comparison of the GppNHp circle Mg^2+- binding pockets of hGBP1^LG (blue) and hGBP1^FL (yellow) highlights the dimerization-induced reorientation of the catalytic Arg 48 and Ser 73 side chains on their corresponding loops. The grey van der Waals surface of monomer B (black) from the hGBP1^LG circle GppNHp dimer is shown to indicate how Arg 48 of monomer A would clash with Thr 133 from monomer B. b, GDP circle AlF[3] from the Ras circle RasGAP complex^16 (orange) is superimposed on GDP circle AlF[3] from hGBP1^LG (green), indicating that the cis 'arginine finger' of hGBP1 (R48) has a similar orientation to that of the trans arginine from RasGAP (R789).

Figure 4.
Figure 4: Structural analysis of the GDPase reaction. a, Superimposition of the active sites of hGBP1^LG circle GMP circle AlF[4]^- (blue) and hGBP1^LG circle GDP circle AlF[3] (green) structures, respectively, showing the shift of GMP for the second hydrolysis step. Black broken lines show stabilizing polar interactions and red broken lines indicate unfavourable vicinities between the nucleotide in the GDP circle AlF[3] structure and the guanine cap residues as found in the GMP circle AlF[4]^- structure. b, Superimposition of nucleotide-binding sites of hGBP1^LG circle GMP (yellow, gold) and Ras circle GDP (green; Protein Data Bank accession code 4Q21) structures with the -phosphate of GMP occupying a similar position to that of the -phosphate of Ras circle GDP. Arg 48 is pointing away from the active site. Red star indicates possible steric hindrance between Lys 117 of the (N/T)KxD motif from Ras and the GMP base conformation found in hGBP1^LG.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 440, 101-104) copyright 2006.

Figures were selected by an automated process.