PDBsum entry 6r3v

Hydrolase

PDB id: 6r3v

Contents

Protein chains

198 a.a.

172 a.a.

Ligands

PO4 ×2

MES

GDP

DTT

Metals

_MG

Waters ×254

PDB id:

6r3v

Name:

Hydrolase

Title:

Crystal structure of rhoa-gdp-pi in complex with rhogap

Structure:

Rho gtpase-activating protein 1. Chain: a. Fragment: gtpase activiting domain. Synonym: cdc42 gtpase-activating protein,gtpase-activating protein rhogap,rho-related small gtpase protein activator,rho-type gtpase- activating protein 1,p50-rhogap. Engineered: yes. Transforming protein rhoa. Chain: b.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: arhgap1, cdc42gap, rhogap1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: rosetta plyss. Gene: rhoa, arh12, arha, rho12.

Resolution:

1.75Å R-factor: 0.178 R-free: 0.207

Authors:

Y.Jin

Key ref:

R.W.Molt et al. (2019). A GAP-GTPase-GDP-P_i Intermediate Crystal Structure Analyzed by DFT Shows GTP Hydrolysis Involves Serial Proton Transfers. Chemistry, 25, 8484-8488. PubMed id: 31038818 DOI: 10.1002/chem.201901627

Date:

21-Mar-19 Release date: 08-May-19

Protein chain

Q07960  (RHG01_HUMAN) -  Rho GTPase-activating protein 1 from Homo sapiens

Seq: 439 a.a.

Struc: 198 a.a.

Protein chain

P61586  (RHOA_HUMAN) -  Transforming protein RhoA from Homo sapiens

Seq: 193 a.a.

Struc: 172 a.a.

Enzyme reactions

• Enzyme class: Chain B: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP + H2O = GDP (Bound ligand (Het Group name = GDP) corresponds exactly) + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1002/chem.201901627

Chemistry 25:8484-8488 (2019)

PubMed id: 31038818

A GAP-GTPase-GDP-P_i Intermediate Crystal Structure Analyzed by DFT Shows GTP Hydrolysis Involves Serial Proton Transfers.

R.W.Molt, E.Pellegrini, Y.Jin.

ABSTRACT

Cell signaling by small G proteins uses an ON to OFF signal based on conformational changes following the hydrolysis of GTP to GDP and release of dihydrogen phosphate (P_i ). The catalytic mechanism of GTP hydrolysis by RhoA is strongly accelerated by a GAP protein and is now well defined, but timing of inorganic phosphate release and signal change remains unresolved. We have generated a quaternary complex for RhoA-GAP-GDP-P_i . Its 1.75 Å crystal structure shows geometry for ionic and hydrogen bond coordination of GDP and P_i in an intermediate state. It enables the selection of a QM core for DFT exploration of a 20 H-bonded network. This identifies serial locations of the two mobile protons from the original nucleophilic water molecule, showing how they move in three rational steps to form a stable quaternary complex. It also suggests how two additional proton transfer steps can facilitate P_i release.