9QZ7 | pdb_00009qz7

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493A structure in complex with 2-methylglyceryl-CoA and inactive cofactor 3-deaza-ThDP

PDB DOI: https://doi.org/10.2210/pdb9QZ7/pdb

Classification: LYASE
Organism(s): Actinomycetospora chiangmaiensis DSM 45062
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-04-22 Released: 2026-02-04
Deposition Author(s): Zahn, M., Rohwerder, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.204 (Depositor), 0.204 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

C2 alpha-carbanion-protonating glutamate discloses tradeoffs between substrate accommodation and reaction rate in actinobacterial 2-hydroxyacyl-CoA lyase.

Zahn, M., Seroka, B., Lazny, R., Lotowski, Z., Rohwerder, T.

(2026) FEBS Open Bio

PubMed: 41606311 Search on PubMed
DOI: https://doi.org/10.1002/2211-5463.70199
Primary Citation Related Structures:
9QZ4, 9QZ5, 9QZ6, 9QZ7

PubMed Abstract:
Thiamine-dependent actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) catalyzes the reversible cleavage of 2-hydroxyacyl-CoAs to formyl-CoA and carbonyl compounds. To exploit the enzyme's biotechnological potential, a deeper understanding of the catalysis is required. Previously, AcHACL E493 was identified as an important acid/base catalyst. Here, wild-type and E493 mutant crystal structures representing Michaelis complexes with 2-hydroxyisobutyryl-CoA and (S)-2-methylglyceryl-CoA are provided. Although E493 guarantees high rates of essential proton transfers in AcAHCL-catalyzed on-pathway cleavage of 2-hydroxyacyl-CoAs and off-pathway carboligations with short-chain aldehydes and ketones, wild-type substrate accommodation is suboptimal. Not E493D, but E493A and E493S mutations improved K _M. However, k _cat is substantially reduced in the mutants. These tradeoffs are discussed by comparing active sites of AcHACL and related enzymes either lacking or possessing an E493 homolog.

Organizational Affiliation

Centre for Enzyme Innovation, School of the Environment and Life Sciences, University of Portsmouth, UK.

Macromolecule Content

Total Structure Weight: 133.27 kDa
Atom Count: 9,841
Modeled Residue Count: 1,148
Deposited Residue Count: 1,224
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-hydroxyacyl-CoA lyase	A, B	612	Actinomycetospora chiangmaiensis DSM 45062	Mutation(s): 1 EC: 4.1
UniProt
Find proteins for P0DUV9 (Actinomycetospora chiangmaiensis (strain DSM 45062 / JCM 15998 / CCTCC AA 205017 / NBRC 104400 / YIM 0006)) Explore P0DUV9 Go to UniProtKB: P0DUV9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DUV9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JCA (Subject of Investigation/LOI) Query on A1JCA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (2~{S})-2-methyl-2,3-bis(oxidanyl)propanethioate C₂₅ H₄₂ N₇ O₁₉ P₃ S ZUNPIMQDZAVEDO-FOXNSAMMSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
TPW (Subject of Investigation/LOI) Query on TPW Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE C₁₃ H₁₉ N₃ O₇ P₂ S IOGGWTLVIZLGGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]