PDBsum entry 6qkt

Hydrolase

PDB id: 6qkt

Contents

Protein chains

297 a.a.

Ligands

GOA

Waters ×629

PDB id:

6qkt

Name:

Hydrolase

Title:

Crystal structure of the fluoroacetate dehalogenase rpa1163 - tyr219phe - fluoroacetate soaked 24hr - glycolate bound

Structure:

Fluoroacetate dehalogenase. Chain: a, b. Engineered: yes

Source:

Rhodopseudomonas palustris. Organism_taxid: 1076. Gene: rpysc3_11920. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.51Å R-factor: 0.178 R-free: 0.205

Authors:

P.Mehrabi,T.H.Kim,R.S.Prosser,E.F.Pai

Key ref:

P.Mehrabi et al. (2019). Substrate-Based Allosteric Regulation of a Homodimeric Enzyme. J Am Chem Soc, 141, 11540-11556. PubMed id: 31188575 DOI: 10.1021/jacs.9b03703

Date:

30-Jan-19 Release date: 26-Jun-19

Protein chains

Q6NAM1  (DEHA_RHOPA) -  Fluoroacetate dehalogenase from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

Seq: 302 a.a.

Struc: 297 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.8.1.3 - haloacetate dehalogenase.
• Reaction: a haloacetate + H2O = a halide anion + glycolate + H⁺

haloacetate + H2O = halide anion + glycolate (Bound ligand (Het Group name = GOA) corresponds exactly) + H(+)

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

Added reference

DOI no: 10.1021/jacs.9b03703

J Am Chem Soc 141:11540-11556 (2019)

PubMed id: 31188575

Substrate-Based Allosteric Regulation of a Homodimeric Enzyme.

P.Mehrabi, C.Di Pietrantonio, T.H.Kim, A.Sljoka, K.Taverner, C.Ing, N.Kruglyak, R.Pomès, E.F.Pai, R.S.Prosser.

ABSTRACT

Many enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an interprotomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by nuclear magnetic resonance and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function.