PDBsum entry 4hlq

Hydrolase activator/protein transport

PDB id: 4hlq

Contents

Protein chains

280 a.a.

172 a.a.

Ligands

SO4 ×5

GDP-BEF ×5

Metals

_MG ×5

Waters ×51

PDB id:

4hlq

Name:

Hydrolase activator/protein transport

Title:

Crystal structure of human rab1b bound to gdp and bef3 in complex with the gap domain of tbc1d20 from homo sapiens

Structure:

Tbc1 domain family member 20. Chain: a, c, e, g, i. Engineered: yes. Ras-related protein rab-1b. Chain: b, d, f, h, j. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: tbc1d20, c20orf140. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rab1b.

Resolution:

3.30Å R-factor: 0.209 R-free: 0.274

Authors:

E.M.Gazdag,K.Gavriljuk,A.Itzen,C.Koetting,K.Gerwert,R.S.Goody

Key ref:

K.Gavriljuk et al. (2012). Catalytic mechanism of a mammalian Rab·RabGAP complex in atomic detail. Proc Natl Acad Sci U S A, 109, 21348-21353. PubMed id: 23236136

Date:

17-Oct-12 Release date: 16-Jan-13

Protein chains

Q96BZ9  (TBC20_HUMAN) -  TBC1 domain family member 20 from Homo sapiens

Seq: 403 a.a.

Struc: 280 a.a.

Protein chains

Q9H0U4  (RAB1B_HUMAN) -  Ras-related protein Rab-1B from Homo sapiens

Seq: 201 a.a.

Struc: 172 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, C, E, G, I: E.C.?
• Enzyme class 3: Chains B, D, F, H, J: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

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.

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

reference

Proc Natl Acad Sci U S A 109:21348-21353 (2012)

PubMed id: 23236136

Catalytic mechanism of a mammalian Rab·RabGAP complex in atomic detail.

K.Gavriljuk, E.M.Gazdag, A.Itzen, C.Kötting, R.S.Goody, K.Gerwert.

ABSTRACT

Rab GTPases, key regulators of vesicular transport, hydrolyze GTP very slowly unless assisted by Rab GTPase-activating proteins (RabGAPs). Dysfunction of RabGAPs is involved in many diseases. By combining X-ray structure analysis and time-resolved FTIR spectroscopy we reveal here the detailed molecular reaction mechanism of a complex between human Rab and RabGAP at the highest possible spatiotemporal resolution and in atomic detail. A glutamine residue of Rab proteins (cis-glutamine) that is essential for intrinsic activity is less important in the GAP-activated reaction. During generation of the RabGAP·Rab:GTP complex, there is a rapid conformational change in which the cis-glutamine is replaced by a glutamine from RabGAP (trans-glutamine); this differs from the RasGAP mechanism, where the cis-glutamine is also important for GAP catalysis. However, as in the case of Ras, a trans-arginine is also recruited to complete the active center during this conformational change. In contrast to the RasGAP mechanism, an accumulation of a state in which phosphate is bound is not observed, and bond breakage is the rate-limiting step. The movement of trans-glutamine and trans-arginine into the catalytic site and bond breakage during hydrolysis are monitored in real time. The combination of X-ray structure analysis and time-resolved FTIR spectroscopy provides detailed insight in the catalysis of human Rab GTPases.