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- PDB-9qz5: Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493S str... -

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Basic information

Entry
Database: PDB / ID: 9qz5
TitleActinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493S structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP
Components2-hydroxyacyl-CoA lyase
KeywordsLYASE / ThDP / CoA / HACL
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases / acetolactate synthase complex / acetolactate synthase activity / L-valine biosynthetic process / : / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / lyase activity / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Chem-3KK / Chem-TPW / 2-hydroxyacyl-CoA lyase
Similarity search - Component
Biological speciesActinomycetospora chiangmaiensis DSM 45062 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.572 Å
AuthorsZahn, M. / Rohwerder, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs Open Bio / Year: 2026
Title: C2 alpha-carbanion-protonating glutamate discloses tradeoffs between substrate accommodation and reaction rate in actinobacterial 2-hydroxyacyl-CoA lyase.
Authors: Zahn, M. / Seroka, B. / Lazny, R. / Lotowski, Z. / Rohwerder, T.
History
DepositionApr 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-hydroxyacyl-CoA lyase
B: 2-hydroxyacyl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,2679
Polymers130,6402
Non-polymers2,6277
Water16,538918
1
A: 2-hydroxyacyl-CoA lyase
B: 2-hydroxyacyl-CoA lyase
hetero molecules

A: 2-hydroxyacyl-CoA lyase
B: 2-hydroxyacyl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,53418
Polymers261,2804
Non-polymers5,25414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area27670 Å2
ΔGint-130 kcal/mol
Surface area62820 Å2
Unit cell
Length a, b, c (Å)103.86, 148.156, 174.576
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 16 - 587 / Label seq-ID: 27 - 598

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein 2-hydroxyacyl-CoA lyase / AcHACL / HACL / 2-hydroxyisobutyryl-CoA lyase


Mass: 65320.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomycetospora chiangmaiensis DSM 45062 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DUV9, Lyases; Carbon-carbon lyases
#2: Chemical ChemComp-TPW / 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / 3-DEAZA-THDP


Mass: 423.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N3O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3KK / S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxy-2-methylpropanethioate / 2-Hydroxyisobutyryl-Coenzyme A


Mass: 853.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O18P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 1500, 0.1 M MIB buffer pH 7.0, 5 mM 3-deazathiamin diphosphate, 1 mM 2-Hydroxyisobutyryl-CoA, 5 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.57→87.29 Å / Num. obs: 89347 / % possible obs: 93.9 % / Redundancy: 11.5 % / CC1/2: 1 / Rrim(I) all: 0.099 / Net I/σ(I): 16.3
Reflection shellResolution: 1.57→1.74 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4469 / CC1/2: 0.7 / Rrim(I) all: 1.538 / % possible all: 59.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.572→87.288 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.903 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.139 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2013 4492 5.028 %
Rwork0.1641 84852 -
all0.166 --
obs-89344 48.079 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.534 Å2
Baniso -1Baniso -2Baniso -3
1-0.056 Å20 Å2-0 Å2
2---0.177 Å2-0 Å2
3---0.121 Å2
Refinement stepCycle: LAST / Resolution: 1.572→87.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8605 0 163 918 9686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128996
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.80912300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36751163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.9575103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.494101358
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.01910406
X-RAY DIFFRACTIONr_chiral_restr0.110.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026936
X-RAY DIFFRACTIONr_nbd_refined0.2090.24788
X-RAY DIFFRACTIONr_nbtor_refined0.3060.26183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2943
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.2154
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.279
X-RAY DIFFRACTIONr_mcbond_it1.1691.5444604
X-RAY DIFFRACTIONr_mcangle_it1.7632.7725756
X-RAY DIFFRACTIONr_scbond_it2.0051.724392
X-RAY DIFFRACTIONr_scangle_it3.0283.0756535
X-RAY DIFFRACTIONr_lrange_it5.0218.12214616
X-RAY DIFFRACTIONr_ncsr_local_group_10.0510.0518797
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.05130.05009
12BX-RAY DIFFRACTIONLocal ncs0.05130.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.572-1.6130.253150.2372930.238136570.9550.9572.25530.223
1.613-1.6570.261410.2437780.244132590.9610.9626.17690.227
1.657-1.7050.248800.23915210.24129660.960.96312.34770.221
1.705-1.7570.2571200.24923820.249125640.9570.9619.9140.225
1.757-1.8150.3011760.24130850.244121990.9490.96326.73170.219
1.815-1.8780.2392150.21236870.214118090.9620.9733.04260.182
1.878-1.9490.2512340.20143130.203113720.9610.97339.98420.17
1.949-2.0290.2432670.19248410.195109880.9610.97546.48710.158
2.029-2.1190.1982650.18251710.183105190.9740.97851.67790.147
2.119-2.2220.2293190.17853550.181100570.9670.9856.41840.144
2.222-2.3430.1983010.16556400.16696020.9780.98261.87250.131
2.343-2.4850.2142920.17458270.17690890.970.98167.32310.141
2.485-2.6560.2383310.18161450.18485760.9650.9875.51310.146
2.656-2.8690.2223520.18164180.18379600.970.9885.05020.146
2.869-3.1420.2233350.1867050.18273690.970.9895.53530.15
3.142-3.5120.213420.16863380.1766800.9720.9831000.149
3.512-4.0550.1812570.14556430.14659000.9820.9881000.138
4.055-4.9630.1372480.1247910.12150390.9880.9921000.119
4.963-7.0080.1822110.14337470.14539580.9810.9891000.143
7.008-87.2880.166910.15421720.15422650.9820.98399.91170.17
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36690.08530.05260.19960.01320.5085-0.0371-0.0123-0.05210.011-0.00730.06670.0754-0.03180.04440.0192-0.00180.02190.0204-0.00520.047427.198320.8-32.5088
20.45570.0732-0.04680.2270.09710.4015-0.0344-0.0506-0.01050.0549-0.0052-0.02410.0140.02880.03960.02190.0088-0.00680.03070.01020.011258.997530.5494-17.459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp15 - 602
2X-RAY DIFFRACTION2ALLBp16 - 602

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