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- PDB-4r3u: Crystal structure of 2-Hydroxyisobutyryl-CoA Mutase -

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Basic information

Entry
Database: PDB / ID: 4r3u
TitleCrystal structure of 2-Hydroxyisobutyryl-CoA Mutase
Components(2-hydroxyisobutyryl-CoA mutase ...) x 2
KeywordsISOMERASE / TIM Rossmann fold / mutase / CoA
Function / homology
Function and homology information


methylmalonyl-CoA mutase activity / Isomerases; Intramolecular transferases; Transferring other groups / cobalamin binding / isomerase activity / metal ion binding
Similarity search - Function
Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. ...Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-HYDROXYBUTANOYL-COENZYME A / Chem-3KK / 5'-DEOXYADENOSINE / COBALAMIN / 2-hydroxyisobutyryl-CoA mutase small subunit / 2-hydroxyisobutyryl-CoA mutase large subunit
Similarity search - Component
Biological speciesAquincola tertiaricarbonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZahn, M. / Kurteva-Yaneva, N. / Rohwerder, T. / Straeter, N.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase.
Authors: Kurteva-Yaneva, N. / Zahn, M. / Weichler, M.T. / Starke, R. / Harms, H. / Muller, R.H. / Strater, N. / Rohwerder, T.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-hydroxyisobutyryl-CoA mutase large subunit
B: 2-hydroxyisobutyryl-CoA mutase large subunit
C: 2-hydroxyisobutyryl-CoA mutase small subunit
D: 2-hydroxyisobutyryl-CoA mutase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,44711
Polymers166,1214
Non-polymers6,3267
Water3,873215
1
A: 2-hydroxyisobutyryl-CoA mutase large subunit
C: 2-hydroxyisobutyryl-CoA mutase small subunit
hetero molecules

A: 2-hydroxyisobutyryl-CoA mutase large subunit
C: 2-hydroxyisobutyryl-CoA mutase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,69812
Polymers166,1214
Non-polymers6,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area21820 Å2
ΔGint-45 kcal/mol
Surface area44810 Å2
MethodPISA
2
B: 2-hydroxyisobutyryl-CoA mutase large subunit
D: 2-hydroxyisobutyryl-CoA mutase small subunit
hetero molecules

B: 2-hydroxyisobutyryl-CoA mutase large subunit
D: 2-hydroxyisobutyryl-CoA mutase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,19610
Polymers166,1214
Non-polymers6,0756
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area20850 Å2
ΔGint-60 kcal/mol
Surface area44680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.030, 119.560, 173.940
Angle α, β, γ (deg.)90.00, 91.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

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2-hydroxyisobutyryl-CoA mutase ... , 2 types, 4 molecules ABCD

#1: Protein 2-hydroxyisobutyryl-CoA mutase large subunit


Mass: 66007.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquincola tertiaricarbonis (bacteria) / Gene: hcmA / Production host: Escherichia coli (E. coli)
References: UniProt: I3VE77, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein 2-hydroxyisobutyryl-CoA mutase small subunit


Mass: 17052.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquincola tertiaricarbonis (bacteria) / Gene: hcmB / Production host: Escherichia coli (E. coli) / References: UniProt: I3VE74

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Non-polymers , 5 types, 222 molecules

#3: Chemical ChemComp-3HC / 3-HYDROXYBUTANOYL-COENZYME A / 3-HYDROXYBUTYRYL-COENZYME A


Mass: 853.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O18P3S
#4: 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
#5: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#6: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 3350, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→24.63 Å / Num. obs: 48815 / % possible obs: 99.9 % / Biso Wilson estimate: 43.67 Å2
Reflection shellResolution: 2.5→2.64 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→24.63 Å / Cor.coef. Fo:Fc: 0.8979 / Cor.coef. Fo:Fc free: 0.8678 / SU R Cruickshank DPI: 0.795 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1519 3.11 %RANDOM
Rwork0.168 ---
obs0.1696 48813 100 %-
Displacement parametersBiso mean: 48.85 Å2
Baniso -1Baniso -2Baniso -3
1--17.5753 Å20 Å211.797 Å2
2--2.3185 Å20 Å2
3---15.2568 Å2
Refine analyzeLuzzati coordinate error obs: 0.353 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10773 0 416 215 11404
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111414HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1715518HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4107SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes287HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1677HARMONIC5
X-RAY DIFFRACTIONt_it11414HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion18.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1514SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance96HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14006SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2598 114 3.15 %
Rwork0.207 3510 -
all0.2086 3624 -
obs--100 %
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)
10.410.18290.21890.9729-0.16151.76050.13740.055-0.0897-0.2297-0.10780.00030.39970.0699-0.0296-0.21990.0860.09690.0194-0.0216-0.029933.3259-7.010568.8097
21.29560.05950.46541.76920.34292.03780.03490.2859-0.0342-0.4958-0.0615-0.0974-0.09250.40480.0265-0.13360.09450.15140.09230.0705-0.101740.123510.02847.6372
31.0503-0.0301-0.52770.5310.24031.4152-0.1299-0.153-0.1104-0.1315-0.00330.0993-0.2517-0.03070.13320.31020.0684-0.1392-0.3040.006-0.292123.592619.079514.595
40.5676-0.3353-0.191200.15811.7483-0.01-0.27280.1902-0.4331-0.0146-0.02-0.4908-0.24680.02460.31030.1537-0.1422-0.2385-0.0773-0.15196.119536.078728.3454
50.1608-0.97720.86911.4081-0.61252.81860.0651-0.03320.0043-0.285-0.06160.081-0.063-0.5303-0.0035-0.18530.09460.04920.1402-0.0390.029910.49729.734955.183
62.9919-0.5335-0.06212.1052-0.45113.6896-0.0683-0.15430.1574-0.2118-0.12580.2816-0.5501-0.45460.1941-0.16860.15440.02640.0553-0.11220.01411.821419.520362.1961
70.0797-0.1085-1.86481.7676-1.7860.81260.0057-0.23830.104-0.0368-0.06540.0696-0.10270.11390.05970.3102-0.0475-0.1388-0.0305-0.1497-0.310234.24135.340437.6735
8-0.1188-1.11052.73767.54061.02062.70790.0428-0.2280.2746-0.106-0.0523-0.0239-0.21760.1970.00950.3102-0.1485-0.1388-0.2396-0.1552-0.310237.354145.313433.0368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - A|476}A2 - 476
2X-RAY DIFFRACTION2{A|477 - A|558}A477 - 558
3X-RAY DIFFRACTION3{B|2 - B|474}B2 - 474
4X-RAY DIFFRACTION4{B|475 - B|558}B475 - 558
5X-RAY DIFFRACTION5{C|3 - C|57}C3 - 57
6X-RAY DIFFRACTION6{C|58 - C|133}C58 - 133
7X-RAY DIFFRACTION7{D|4 - D|53}D4 - 53
8X-RAY DIFFRACTION8{D|54 - D|132}D54 - 132

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