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- PDB-9qz4: Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493D str... -

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Basic information

Entry
Database: PDB / ID: 9qz4
TitleActinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493D 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 / isoleucine 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: 1.63 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

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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)133,34710
Polymers130,6962
Non-polymers2,6518
Water17,853991
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)266,69520
Polymers261,3924
Non-polymers5,30216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area27930 Å2
ΔGint-145 kcal/mol
Surface area62670 Å2
Unit cell
Length a, b, c (Å)103.98, 147.528, 174.449
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
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: 65348.121 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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
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: Jul 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.63→87.23 Å / Num. obs: 83484 / % possible obs: 94.7 % / Redundancy: 11.6 % / CC1/2: 1 / Rrim(I) all: 0.13 / Net I/σ(I): 12.7
Reflection shellResolution: 1.63→1.83 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4174 / CC1/2: 0.7 / Rrim(I) all: 1.669 / % possible all: 67.4

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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: 1.63→87.225 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.319 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.141 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1928 4194 5.024 %
Rwork0.1574 79289 -
all0.159 --
obs-83483 50.235 %
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: 24.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.096 Å20 Å20 Å2
2---0.277 Å2-0 Å2
3---0.181 Å2
Refinement stepCycle: LAST / Resolution: 1.63→87.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8609 0 164 991 9764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128939
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.80812209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37951145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.0985102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.305101344
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.58210400
X-RAY DIFFRACTIONr_chiral_restr0.1090.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026874
X-RAY DIFFRACTIONr_nbd_refined0.2060.24659
X-RAY DIFFRACTIONr_nbtor_refined0.3040.26125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2930
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.285
X-RAY DIFFRACTIONr_mcbond_it1.3071.7394586
X-RAY DIFFRACTIONr_mcangle_it1.9273.1235729
X-RAY DIFFRACTIONr_scbond_it2.3911.944353
X-RAY DIFFRACTIONr_scangle_it3.63.4646480
X-RAY DIFFRACTIONr_lrange_it5.40920.91614363
X-RAY DIFFRACTIONr_ncsr_local_group_10.0490.0518696
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.048510.05009
12BX-RAY DIFFRACTIONLocal ncs0.048510.05009
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
1.63-1.6720.231100.2362600.236122370.9760.9622.20640.226
1.672-1.7180.238360.2325610.233118490.9610.9615.03840.218
1.718-1.7680.252550.2549970.254115970.9620.9579.07130.238
1.768-1.8220.235950.25117200.25111830.9610.9616.230.23
1.822-1.8820.2841310.22527250.228109250.9480.96826.14190.203
1.882-1.9480.2391920.21734110.218105290.9620.9734.21980.192
1.948-2.0220.2312510.20540780.207101860.9640.97342.49950.179
2.022-2.1040.2572370.19645820.19998380.960.97548.98350.167
2.104-2.1980.2332580.18148250.18394090.9680.97954.02270.153
2.198-2.3050.2022610.16951300.1790060.9750.98259.86010.14
2.305-2.4290.2332700.17854660.1885950.9670.9866.73650.148
2.429-2.5770.2443300.18459380.18781170.9630.97877.22060.15
2.577-2.7540.2453490.17963880.18376370.9640.9888.21530.147
2.754-2.9750.23400.17466640.17571230.9760.98198.32940.143
2.975-3.2580.1993200.16362730.16465940.9750.98499.98480.143
3.258-3.6420.1832930.14656640.14859610.9810.98899.93290.137
3.642-4.2040.1612460.13250380.13352840.9860.9911000.127
4.204-5.1460.1332180.11142910.11245090.9890.9931000.11
5.146-7.2650.1681870.13733420.13935300.9850.9999.97170.137
7.265-87.2250.1491150.14619350.14620510.9870.98399.95120.164
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)
10.30920.07510.04010.1860.01680.4691-0.0362-0.0109-0.0460.0081-0.00840.05620.0747-0.03940.04460.0194-0.00380.020.0216-0.0070.0392-24.7278-53.1361-32.4487
20.39520.0812-0.0530.19830.08710.3966-0.0299-0.0564-0.00810.0495-0.0056-0.01860.01860.03490.03550.02050.0085-0.00560.03180.010.00937.1024-43.3559-17.4526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp15 - 602
2X-RAY DIFFRACTION2ALLBp16 - 602

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