PDBsum entry 5u99

Transferase

PDB id: 5u99

Contents

Protein chain

278 a.a.

Ligands

SO4 ×3

ATP

Metals

_MG ×2

Waters ×28

PDB id:

5u99

Name:

Transferase

Title:

Transition state analysis of adenosine triphosphate phosphoribosyltransferase

Structure:

Atp phosphoribosyltransferase. Chain: a. Synonym: atp-prtase. Engineered: yes

Source:

Mycobacterium tuberculosis (strain atcc 25618 / h37rv). Organism_taxid: 83332. Strain: atcc 25618 / h37rv. Gene: hisg, rv2121c, mtcy261.17c. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Expression_system_variant: plyss. Expression_system_cell_line: bl21 star

Resolution:

2.40Å R-factor: 0.217 R-free: 0.251

Authors:

G.-J.Moggre,M.B.Poulin,P.C.Tyler,V.L.Schramm,E.J.Parker

Key ref:

G.J.Moggré et al. (2017). Transition State Analysis of Adenosine Triphosphate Phosphoribosyltransferase. ACS Chem Biol, 12, 2662-2670. PubMed id: 28872824 DOI: 10.1021/acschembio.7b00484

Date:

15-Dec-16 Release date: 20-Sep-17

Protein chain

P9WMN1  (HIS1_MYCTU) -  ATP phosphoribosyltransferase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 284 a.a.

Struc: 278 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.2.17 - Atp phosphoribosyltransferase.
• Pathway: Histidine Biosynthesis (early stages)
• Reaction: 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP

1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP (Bound ligand (Het Group name = ATP) corresponds exactly)

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

reference

DOI no: 10.1021/acschembio.7b00484

ACS Chem Biol 12:2662-2670 (2017)

PubMed id: 28872824

Transition State Analysis of Adenosine Triphosphate Phosphoribosyltransferase.

G.J.Moggré, M.B.Poulin, P.C.Tyler, V.L.Schramm, E.J.Parker.

ABSTRACT

Adenosine triphosphate phosphoribosyltransferase (ATP-PRT) catalyzes the first step in histidine biosynthesis, a pathway essential to microorganisms and a validated target for antimicrobial drug design. The ATP-PRT enzyme catalyzes the reversible substitution reaction between phosphoribosyl pyrophosphate and ATP. The enzyme exists in two structurally distinct forms, a short- and a long-form enzyme. These forms share a catalytic core dimer but bear completely different allosteric domains and thus distinct quaternary assemblies. Understanding enzymatic transition states can provide essential information on the reaction mechanisms and insight into how differences in domain structure influence the reaction chemistry, as well as providing a template for inhibitor design. In this study, the transition state structures for ATP-PRT enzymes from Campylobacter jejuni and Mycobacterium tuberculosis (long-form enzymes) and from Lactococcus lactis (short-form) were determined and compared. Intrinsic kinetic isotope effects (KIEs) were obtained at reaction sensitive positions for the reverse reaction using phosphonoacetic acid, an alternative substrate to the natural substrate pyrophosphate. The experimental KIEs demonstrated mechanistic similarities between the three enzymes and provided experimental boundaries for quantum chemical calculations to characterize the transition states. Predicted transition state structures support a dissociative reaction mechanism with a D_N*A_N^‡transition state. Weak interactions from the incoming nucleophile and a fully dissociated ATP adenine are predicted regardless of the difference in overall structure and quaternary assembly. These studies establish that despite significant differences in the quaternary assembly and regulatory machinery between ATP-PRT enzymes from different sources, the reaction chemistry and catalytic mechanism are conserved.