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- PDB-6oxd: Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase ... -

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Basic information

Entry
Database: PDB / ID: 6oxd
TitleStructure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin
Components(Methylmalonyl-CoA mutase ...) x 2
KeywordsISOMERASE / methylmalonyl CoA mutase / methylmalonyl CoA mutase deficiency / metabolic disease / cobalamin / cobalt / disease mutation / metal-binding / itaconyl CoA / radical / Mycobacterium tuberculosis / immunometabolite / B12 / methylmalonic aciduria
Function / homology
Function and homology information


lactate fermentation to propionate and acetate / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / methylmalonyl-CoA mutase activity / cobalamin binding / peptidoglycan-based cell wall / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Methylmalonyl-CoA mutase, beta chain / Methylmalonyl-CoA mutase signature. / 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 (vitamin B12)-dependent enzyme, catalytic / Cobalamin-binding domain / B12 binding domain ...Methylmalonyl-CoA mutase, beta chain / Methylmalonyl-CoA mutase signature. / 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 (vitamin B12)-dependent enzyme, catalytic / Cobalamin-binding domain / 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
5'-DEOXYADENOSINE / COBALAMIN / : / Itaconyl coenzyme A / Methylmalonyl-CoA mutase small subunit / Probable methylmalonyl-CoA mutase large subunit / Probable methylmalonyl-CoA mutase large subunit / Probable methylmalonyl-CoA mutase small subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPurchal, M. / Ruetz, M. / Banerjee, R. / Koutmos, M.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Science / Year: 2019
Title: Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair.
Authors: Ruetz, M. / Campanello, G.C. / Purchal, M. / Shen, H. / McDevitt, L. / Gouda, H. / Wakabayashi, S. / Zhu, J. / Rubin, E.J. / Warncke, K. / Mootha, V.K. / Koutmos, M. / Banerjee, R.
History
DepositionMay 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylmalonyl-CoA mutase large subunit
B: Methylmalonyl-CoA mutase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,0646
Polymers145,5612
Non-polymers2,5024
Water20,1771120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-56 kcal/mol
Surface area45300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.576, 104.957, 194.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Methylmalonyl-CoA mutase ... , 2 types, 2 molecules AB

#1: Protein Methylmalonyl-CoA mutase large subunit / Methylmalonyl-CoA mutase large subunit MutB (Mcm) / Putative methylmalonyl-CoA mutase large subunit ...Methylmalonyl-CoA mutase large subunit MutB (Mcm) / Putative methylmalonyl-CoA mutase large subunit MutB (Mcm) / Methylmalonyl-CoA mutase / Chain A


Mass: 80692.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: mutB, DK316_08225, DSI35_00620, ERS027651_01113, ERS027652_00280, ERS124361_00189, SAMEA2682864_01878, SAMEA2683035_01024
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A0E8UW09, UniProt: P9WJK5*PLUS, methylmalonyl-CoA mutase
#2: Protein Methylmalonyl-CoA mutase small subunit / Methylmalonyl-CoA mutase small subunit mutA


Mass: 64869.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: mutA, DK316_08220, ERS007663_02000, ERS023446_02236, ERS027651_01114, ERS027656_01366, ERS124361_00188, SAMEA2682864_01877, SAMEA2683035_01025
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045IZR3, UniProt: P9WJK7*PLUS, methylmalonyl-CoA mutase

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Non-polymers , 5 types, 1124 molecules

#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NJS / Itaconyl coenzyme A


Mass: 881.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H42N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1120 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.4 M sodium phosphate monobasic, 1.6 M potassium phosphate dibasic, 0.1 M imidazole/HCl, pH 8, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2018
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→29.8 Å / Num. obs: 104126 / % possible obs: 98.4 % / Redundancy: 4.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.127 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.997 / Num. unique obs: 5172 / CC1/2: 0.622 / Rrim(I) all: 1.243 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2REQ

2req


Resolution: 2→29.798 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9
RfactorNum. reflection% reflection
Rfree0.1968 5352 5.14 %
Rwork0.159 --
obs0.1609 104041 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9968 0 166 1122 11256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01610365
X-RAY DIFFRACTIONf_angle_d1.55214163
X-RAY DIFFRACTIONf_dihedral_angle_d14.1946184
X-RAY DIFFRACTIONf_chiral_restr0.141610
X-RAY DIFFRACTIONf_plane_restr0.0111872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.32271650.28293331X-RAY DIFFRACTION100
2.0227-2.04650.34171910.27323270X-RAY DIFFRACTION100
2.0465-2.07150.32821630.26523327X-RAY DIFFRACTION99
2.0715-2.09770.2981820.2493280X-RAY DIFFRACTION99
2.0977-2.12530.23031700.22633321X-RAY DIFFRACTION100
2.1253-2.15440.27111720.21813289X-RAY DIFFRACTION100
2.1544-2.18520.24621840.20513350X-RAY DIFFRACTION100
2.1852-2.21780.26651930.19383253X-RAY DIFFRACTION99
2.2178-2.25240.22631780.1923326X-RAY DIFFRACTION99
2.2524-2.28930.20661660.17823332X-RAY DIFFRACTION99
2.2893-2.32880.2331990.18083293X-RAY DIFFRACTION99
2.3288-2.37110.23851890.18073281X-RAY DIFFRACTION99
2.3711-2.41670.22771870.17773291X-RAY DIFFRACTION99
2.4167-2.4660.22761890.17063328X-RAY DIFFRACTION99
2.466-2.51960.19111780.16443277X-RAY DIFFRACTION99
2.5196-2.57820.20861780.15433307X-RAY DIFFRACTION99
2.5782-2.64260.19641750.15493283X-RAY DIFFRACTION98
2.6426-2.7140.19931850.15133310X-RAY DIFFRACTION99
2.714-2.79380.21071710.1623291X-RAY DIFFRACTION99
2.7938-2.88390.21441830.15993291X-RAY DIFFRACTION98
2.8839-2.98690.20971790.1623298X-RAY DIFFRACTION98
2.9869-3.10640.19531910.15973248X-RAY DIFFRACTION97
3.1064-3.24760.18131740.15913321X-RAY DIFFRACTION98
3.2476-3.41860.19041780.14793235X-RAY DIFFRACTION96
3.4186-3.63250.17811790.14113251X-RAY DIFFRACTION96
3.6325-3.91230.1571480.12583283X-RAY DIFFRACTION96
3.9123-4.3050.14541960.11833243X-RAY DIFFRACTION95
4.305-4.92550.13451750.11353230X-RAY DIFFRACTION94
4.9255-6.19650.16721630.14083251X-RAY DIFFRACTION93
6.1965-29.80170.1891710.16053298X-RAY DIFFRACTION91

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