8VZI | pdb_00008vzi

Crystal Structure of 2-Hydroxyacyl-CoA Lyase/Synthase CcHACS from Conidiobolus coronatus in the Complex with THDP and ADP

• PDB DOI: https://doi.org/10.2210/pdb8VZI/pdb

• Classification: LYASE
• Organism(s): Conidiobolus coronatus NRRL 28638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-11 Released: 2024-10-02 
• Deposition Author(s): Kim, Y., Gade, P., Endres, M., Lee, S., Yoshikuni, Y., Gonzalez, R., Michalska, K., Joachimiak, A.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: in silico

Literature

Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family.

Kim, Y., Lee, S.H., Gade, P., Nattermann, M., Maltseva, N., Endres, M., Chen, J., Wichmann, P., Hu, Y., Marchal, D.G., Yoshikuni, Y., Erb, T.J., Gonzalez, R., Michalska, K., Joachimiak, A.

(2024) Commun Chem 7: 160-160

• PubMed: 39034323 
• DOI: https://doi.org/10.1038/s42004-024-01242-y
• Primary Citation Related Structures: 
  8VZA, 8VZB, 8VZC, 8VZD, 8VZE, 8VZF, 8VZH, 8VZI, 8VZJ, 8VZK


• PubMed Abstract: 
  

  2-Hydroxyacyl-CoA lyase/synthase (HACL/S) is a thiamine diphosphate (ThDP)-dependent versatile enzyme originally discovered in the mammalian α-oxidation pathway. HACL/S natively cleaves 2-hydroxyacyl-CoAs and, in its reverse direction, condenses formyl-CoA with aldehydes or ketones. The one-carbon elongation biochemistry based on HACL/S has enabled the use of molecules derived from greenhouse gases as biomanufacturing feedstocks. We investigated several HACL/S family members with high activity in the condensation of formyl-CoA and aldehydes, and distinct chain-length specificities and kinetic parameters. Our analysis revealed the structures of enzymes in complex with acyl-CoA substrates and products, several covalent intermediates, bound ThDP and ADP, as well as the C-terminal active site region. One of these observed states corresponds to the intermediary α-carbanion with hydroxymethyl-CoA covalently attached to ThDP. This research distinguishes HACL/S from related sub-families and identifies key residues involved in substrate binding and catalysis. These findings expand our knowledge of acyloin-condensation biochemistry and offer attractive prospects for biocatalysis using carbon elongation.

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Organizational Affiliation: 
• eBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA.
Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.
Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA. [e-mail].
eBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA. [e-mail].
Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA. [e-mail].
eBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA. [e-mail].
Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA. [e-mail].
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 251.35 kDa 
• Atom Count: 18,554 
• Modeled Residue Count: 2,155 
• Deposited Residue Count: 2,252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-hydroxyacyl-CoA lyase-like protein 1	A, B, C, D	563	Conidiobolus coronatus NRRL 28638	Mutation(s): 0  Gene Names: CONCODRAFT_4597 EC: 4.1.2.63
UniProt
Find proteins for A0A137PC97 (Conidiobolus coronatus (strain ATCC 28846 / CBS 209.66 / NRRL 28638)) Explore A0A137PC97  Go to UniProtKB:  A0A137PC97

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	AA [auth C], F [auth A], LA [auth D], Q [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
TPP (Subject of Investigation/LOI)	E [auth A], KA [auth D], P [auth B], Z [auth C]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
ALA	I [auth A], J [auth A], K [auth A]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
GLY	T [auth B]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO	BA [auth C], CA [auth C], G [auth A], H [auth A], M [auth A], MA [auth D], OA [auth D], PA [auth D], R [auth B], S [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	GA [auth C], IA [auth C], L [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	DA [auth C], EA [auth C], FA [auth C], HA [auth C], NA [auth D], U [auth B], V [auth B], W [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	O [auth A], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	JA [auth C], N [auth A], QA [auth D], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.742	α = 90
b = 179.286	β = 108.23
c = 96.826	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Kim, Y., Gade, P., Endres, M., Lee, S., Yoshikuni, Y., Gonzalez, R., Michalska, K., Joachimiak, A.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release