2AF4

Phosphotransacetylase from Methanosarcina thermophila co-crystallized with coenzyme A

DOI: 10.2210/pdb2AF4/pdb

Classification: TRANSFERASE
Organism(s): Methanosarcina thermophila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-07-25 Released: 2006-01-24
Deposition Author(s): Lawrence, S.H., Luther, K.B., Ferry, J.G., Schindelin, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.272
R-Value Work: 0.203
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural and functional studies suggest a catalytic mechanism for the phosphotransacetylase from Methanosarcina thermophila.

Lawrence, S.H., Luther, K.B., Schindelin, H., Ferry, J.G.

(2006) J Bacteriol 188: 1143-1154

PubMed: 16428418 Search on PubMedSearch on PubMed Central
DOI: 10.1128/JB.188.3.1143-1154.2006
Primary Citation of Related Structures:
2AF4, 2AF3

PubMed Abstract:

Phosphotransacetylase (EC 2.3.1.8) catalyzes reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. Two crystal structures of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila in complex with the substrate CoA revealed one CoA (CoA1) bound in the proposed active site cleft and an additional CoA (CoA2) bound at the periphery of the cleft. The results of isothermal titration calorimetry experiments are described, and they support the hypothesis that there are distinct high-affinity (equilibrium dissociation constant [KD], 20 microM) and low-affinity (KD, 2 mM) CoA binding sites. The crystal structures indicated that binding of CoA1 is mediated by a series of hydrogen bonds and extensive van der Waals interactions with the enzyme and that there are fewer of these interactions between CoA2 and the enzyme. Different conformations of the protein observed in the crystal structures suggest that domain movements which alter the geometry of the active site cleft may contribute to catalysis. Kinetic and calorimetric analyses of site-specific replacement variants indicated that there are catalytic roles for Ser309 and Arg310, which are proximal to the reactive sulfhydryl of CoA1. The reaction is hypothesized to proceed through base-catalyzed abstraction of the thiol proton of CoA by the adjacent and invariant residue Asp316, followed by nucleophilic attack of the thiolate anion of CoA on the carbonyl carbon of acetyl phosphate. We propose that Arg310 binds acetyl phosphate and orients it for optimal nucleophilic attack. The hypothesized mechanism proceeds through a negatively charged transition state stabilized by hydrogen bond donation from Ser309.

Related Citations:

Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila
Iyer, P.P., Lawrence, S.H., Luther, K.B., Rajashankar, K.R., Yennawar, H.P., Ferry, J.G., Schindelin, H.
(2004) Structure 12: 559

Organizational Affiliation:

Department of Biochemistry, Center for Structural Biology, SUNY Stony Brook, Stony Brook, NY 11794-5115, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate acetyltransferase	C, D	333	Methanosarcina thermophila	Mutation(s): 1 Gene Names: pta EC: 2.3.1.8
Find proteins for P38503 (Methanosarcina thermophila) Explore P38503 Go to UniProtKB: P38503
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain C [C] SDF format, chain D [D] MOL2 format, chain C [C] MOL2 format, chain D [D]	C, D	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Ligand Interaction