6HE2

Crystal structure of an open conformation of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in complex with 2-HIB-AMP and CoA

Summary for 6HE2

• Entry DOI: 10.2210/pdb6he2/pdb
• Descriptor: 2-hydroxyisobutyryl-CoA synthetase, ADENOSINE MONOPHOSPHATE, [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 2-methyl-2-oxidanyl-propanoate, ... (5 entities in total)
• Functional Keywords: ligase, 2-hydroxyisobutyrate coa
• Biological source: Aquincola tertiaricarbonis
• Total number of polymer chains: 2
• Total formula weight: 114982.25

Authors

Zahn, M.,Rohwerder, T.,Strater, N. (deposition date: 2018-08-20, release date: 2019-08-28, Last modification date: 2024-01-17)

Primary citation

Zahn, M.,Kurteva-Yaneva, N.,Schuster, J.,Krug, U.,Georgi, T.,Muller, R.H.,Rohwerder, T.,Strater, N.
Structures of 2-Hydroxyisobutyric Acid-CoA Ligase Reveal Determinants of Substrate Specificity and Describe a Multi-Conformational Catalytic Cycle.
J.Mol.Biol., 431:2747-2761, 2019

PubMed Abstract: 2-Hydroxyisobutyric acid (2-HIBA) is a biomarker of adiposity and associated metabolic diseases such as diabetes mellitus. It is also formed in the bacterial degradation pathway of the fuel oxygenate methyl tert-butyl ether (MTBE), requiring thioesterification with CoA prior to isomerization to 3-hydroxybutyryl-CoA by B-dependent acyl-CoA mutases. Here, we identify the adenylating enzymes superfamily member 2-HIBA-CoA ligase (HCL) in the MTBE-degrading bacterium Aquincola tertiaricarbonis L108 by knockout experiments. To characterize this central enzyme of 2-HIBA metabolism, ligase activity kinetics of purified HCL and its X-ray crystal structures were studied. We analyzed the enzyme in three states, which differ in the orientation of the two enzyme domains. A 154° rotation of the C-terminal domain accompanies the switch from the adenylate- into the thioester-forming state. Furthermore, a third conformation was obtained, which differs by 50° and 130° from the adenylation and thioesterification states, respectively. Phylogenetic and structural analysis reveals that HCL defines a new subgroup within phenylacetate-CoA ligases (PCLs) thus far described to exclusively accept aromatic acyl substrates. In contrast, kinetic characterization clearly demonstrated that HCL catalyzes CoA activation of several aliphatic short-chain carboxylic acids, preferentially 2-HIBA. Compared to the classical PCL representatives PaaK1 and PaaK2 of Burkholderia cenocepacia J2315, the acyl binding pocket of HCL is significantly smaller and more polar, due to unique active-site residues Y164 and S239 forming H-bonds with the OH-group of the acyl substrate moiety. Furthermore, HCL and PaaK topologies illustrate the evolutionary steps leading from a homodimeric to the fused monomeric core fold found in other ligases.

PubMed: 31145912
DOI: 10.1016/j.jmb.2019.05.027

Experimental method

X-RAY DIFFRACTION (2.3 Å)