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

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Basic information

Entry
Database: PDB / ID: 6oxc
TitleStructure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin
Components
  • Methylmalonyl-CoA mutase large subunit
  • Methylmalonyl-CoA mutase small subunit mutA
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 / 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: 1.9 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 mutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,1434
Polymers145,5612
Non-polymers1,5822
Water24,9511385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-59 kcal/mol
Surface area48070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.802, 103.561, 211.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 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, 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
#3: Chemical ChemComp-B12 / COBALAMIN


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


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1385 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM sodium cacodylate/HCl, pH 6.5, 800 mM sodium citrate tribasic dihydrate, 0.05% w/v casein, 0.05% w/v hemoglobin, 0.0005% w/v pepsin, 0.0005% w/v protease, 0.0005% w/v Proteinase K, 0. ...Details: 100 mM sodium cacodylate/HCl, pH 6.5, 800 mM sodium citrate tribasic dihydrate, 0.05% w/v casein, 0.05% w/v hemoglobin, 0.0005% w/v pepsin, 0.0005% w/v protease, 0.0005% w/v Proteinase K, 0.0005% w/v trypsin, 0.002 M HEPES sodium, pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 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: 1.9→29.1 Å / Num. obs: 129672 / % possible obs: 96.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 24.6 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.16 / Net I/σ(I): 7.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6274 / CC1/2: 0.636 / Rrim(I) all: 1.104 / % possible all: 95.4

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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: 1.9→28.967 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 6579 5.08 %
Rwork0.1618 --
obs0.1639 129577 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→28.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10035 0 0 1385 11420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110261
X-RAY DIFFRACTIONf_angle_d1.24414011
X-RAY DIFFRACTIONf_dihedral_angle_d12.0876119
X-RAY DIFFRACTIONf_chiral_restr0.1361593
X-RAY DIFFRACTIONf_plane_restr0.0081859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.28632140.24433965X-RAY DIFFRACTION95
1.9216-1.94420.27442330.24693994X-RAY DIFFRACTION95
1.9442-1.96790.28332070.23273994X-RAY DIFFRACTION95
1.9679-1.99280.27962300.21214043X-RAY DIFFRACTION95
1.9928-2.0190.27042280.20623922X-RAY DIFFRACTION95
2.019-2.04670.2342340.19533995X-RAY DIFFRACTION94
2.0467-2.07590.2432150.19394012X-RAY DIFFRACTION95
2.0759-2.10690.25082010.19294053X-RAY DIFFRACTION95
2.1069-2.13980.22762330.19284007X-RAY DIFFRACTION96
2.1398-2.17490.2661910.19034098X-RAY DIFFRACTION96
2.1749-2.21230.23542130.19294075X-RAY DIFFRACTION96
2.2123-2.25260.23792090.18324100X-RAY DIFFRACTION97
2.2526-2.29590.22552170.18134087X-RAY DIFFRACTION96
2.2959-2.34270.24422110.18994061X-RAY DIFFRACTION96
2.3427-2.39360.23222360.18364067X-RAY DIFFRACTION96
2.3936-2.44930.21542150.18074018X-RAY DIFFRACTION95
2.4493-2.51050.2251990.18213918X-RAY DIFFRACTION92
2.5105-2.57830.21812080.18044083X-RAY DIFFRACTION96
2.5783-2.65420.22032050.18174158X-RAY DIFFRACTION97
2.6542-2.73980.25392260.17824157X-RAY DIFFRACTION98
2.7398-2.83760.20852110.17354107X-RAY DIFFRACTION96
2.8376-2.95110.19722330.15664168X-RAY DIFFRACTION97
2.9511-3.08530.19712570.15744143X-RAY DIFFRACTION98
3.0853-3.24770.19911910.15354236X-RAY DIFFRACTION97
3.2477-3.45090.2012160.14424209X-RAY DIFFRACTION98
3.4509-3.71690.16042310.13184200X-RAY DIFFRACTION97
3.7169-4.090.17272130.12184210X-RAY DIFFRACTION97
4.09-4.67960.13942270.11264171X-RAY DIFFRACTION96
4.6796-5.88770.14222250.1324305X-RAY DIFFRACTION97
5.8877-28.97010.18232500.16544442X-RAY DIFFRACTION98

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