8VZB

Crystal Structure of 2-Hydroxacyl-CoA Lyase/Synthase ApbHACS from Alphaproteobacteria bacterium in the Complex with THDP, D-Lactyl-CoA, and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: in silico
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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

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

  • DOI: https://doi.org/10.1038/s42004-024-01242-y
  • Primary Citation of 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.


  • Organizational Affiliation

    eBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxalyl-CoA decarboxylase
A, B, C, D
560Alphaproteobacteria bacteriumMutation(s): 0 
Gene Names: DCO82_10540
EC: 4.1.1.8
UniProt
Find proteins for A0A3C0TX30 (Alphaproteobacteria bacterium)
Explore A0A3C0TX30 
Go to UniProtKB:  A0A3C0TX30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3C0TX30
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UQ3 (Subject of Investigation/LOI)
Query on UQ3

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BA [auth C],
G [auth A],
LA [auth D],
R [auth B]
S-{(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (2R)-2-hydroxypropanethioate
C24 H40 N7 O18 P3 S
VIWKEBOLLIEAIL-AGCMQPJKSA-N
8FL (Subject of Investigation/LOI)
Query on 8FL

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AA [auth C],
F [auth A],
KA [auth D],
Q [auth B]
2-[(2R)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-oxidanyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate
C12 H20 N4 O8 P2 S
GFCMTWPFATXWRY-GFCCVEGCSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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CA [auth C],
H [auth A],
MA [auth D],
S [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PEG
Query on PEG

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FA [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

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DA [auth C]
EA [auth C]
IA [auth C]
L [auth A]
M [auth A]
DA [auth C],
EA [auth C],
IA [auth C],
L [auth A],
M [auth A],
O [auth A],
OA [auth D],
PA [auth D],
SA [auth D],
U [auth B],
V [auth B],
W [auth B],
Y [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

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GA [auth C]
I [auth A]
K [auth A]
QA [auth D]
RA [auth D]
GA [auth C],
I [auth A],
K [auth A],
QA [auth D],
RA [auth D],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY (Subject of Investigation/LOI)
Query on ACY

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J [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
ACE
Query on ACE

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NA [auth D],
T [auth B]
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
CL
Query on CL

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HA [auth C],
N [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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E [auth A],
JA [auth D],
P [auth B],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.709α = 90
b = 178.005β = 90
c = 196.111γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
XDSdata scaling
HKL-3000phasing
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

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