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- PDB-9qz6: Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in com... -

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Basic information

Entry
Database: PDB / ID: 9qz6
TitleActinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with 2-methylglyceryl-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-TPW / 2-hydroxyacyl-CoA lyase
Similarity search - Component
Biological speciesActinomycetospora chiangmaiensis DSM 45062 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 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

Downloads & links

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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)133,3839
Polymers130,7242
Non-polymers2,6597
Water19,1861065
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)266,76618
Polymers261,4494
Non-polymers5,31814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area27560 Å2
ΔGint-126 kcal/mol
Surface area62910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.768, 146.493, 174.321
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: 65362.152 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1JCA / ~{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


Mass: 869.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1065 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
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-methylglyceryl-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: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.551→84.68 Å / Num. obs: 104204 / % possible obs: 92.3 % / Redundancy: 13.8 % / CC1/2: 1 / Rrim(I) all: 0.102 / Net I/σ(I): 18.7
Reflection shellResolution: 1.551→1.694 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5211 / CC1/2: 0.64 / Rrim(I) all: 1.682 / % possible all: 72.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.551→84.68 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.441 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.112 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1841 5203 4.993 %
Rwork0.1577 99001 -
all0.159 --
obs-104204 54.642 %
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: 22.955 Å2
Baniso -1Baniso -2Baniso -3
1--0.064 Å2-0 Å2-0 Å2
2--0.139 Å20 Å2
3----0.075 Å2
Refinement stepCycle: LAST / Resolution: 1.551→84.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8618 0 165 1065 9848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0128991
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.8112273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39751156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.0485102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.765101353
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.14610404
X-RAY DIFFRACTIONr_chiral_restr0.1130.21397
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026914
X-RAY DIFFRACTIONr_nbd_refined0.2080.24746
X-RAY DIFFRACTIONr_nbtor_refined0.3090.26216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.21014
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.2155
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.290
X-RAY DIFFRACTIONr_mcbond_it1.2691.5364600
X-RAY DIFFRACTIONr_mcangle_it1.872.7555749
X-RAY DIFFRACTIONr_scbond_it2.4441.7594391
X-RAY DIFFRACTIONr_scangle_it3.6073.1266519
X-RAY DIFFRACTIONr_lrange_it5.9118.99714663
X-RAY DIFFRACTIONr_ncsr_local_group_10.0530.0518710
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.052910.05009
12BX-RAY DIFFRACTIONLocal ncs0.052910.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.551-1.5910.362250.259584X-RAY DIFFRACTION4.3606
1.591-1.6350.275740.2571517X-RAY DIFFRACTION11.6301
1.635-1.6820.2711110.242252X-RAY DIFFRACTION17.842
1.682-1.7340.2481670.2243058X-RAY DIFFRACTION24.9787
1.734-1.7910.2722060.2143705X-RAY DIFFRACTION31.2081
1.791-1.8540.2452240.1944223X-RAY DIFFRACTION36.7855
1.854-1.9240.2052580.1814847X-RAY DIFFRACTION43.696
1.924-2.0020.2232950.1765311X-RAY DIFFRACTION49.6722
2.002-2.0910.1872840.1775818X-RAY DIFFRACTION56.5105
2.091-2.1930.2083040.1756514X-RAY DIFFRACTION65.9062
2.193-2.3120.2183580.1757153X-RAY DIFFRACTION76.4712
2.312-2.4520.2064070.1817854X-RAY DIFFRACTION88.5423
2.452-2.6210.2084220.1798196X-RAY DIFFRACTION98.2444
2.621-2.8310.2053950.1657730X-RAY DIFFRACTION99.267
2.831-3.1010.1763870.1567137X-RAY DIFFRACTION99.458
3.101-3.4660.1783350.1526478X-RAY DIFFRACTION99.5034
3.466-4.0010.1633190.1345730X-RAY DIFFRACTION99.6705
4.001-4.8980.1452900.1174860X-RAY DIFFRACTION99.8255
4.898-6.9150.1652120.1413835X-RAY DIFFRACTION99.8766
6.915-84.680.1511300.1532199X-RAY DIFFRACTION99.9142
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)
10.3654-0.09190.03110.2355-0.03260.496-0.04410.0053-0.0438-0.0048-0.0062-0.07440.06970.04330.05030.01710.00470.0180.01410.00630.043724.693320.569832.4393
20.4333-0.0968-0.05930.256-0.09560.4115-0.03290.0678-0.0123-0.0605-0.00460.03120.0177-0.04330.03750.0234-0.0091-0.00920.03-0.00920.0119-7.100829.927817.4412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp14 - 601
2X-RAY DIFFRACTION2ALLBp16 - 601

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