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- PDB-8dyl: Crystal structure of human methylmalonyl-CoA mutase bound to aquo... -

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Basic information

Entry
Database: PDB / ID: 8dyl
TitleCrystal structure of human methylmalonyl-CoA mutase bound to aquocobalamin
ComponentsMethylmalonyl-CoA mutase, mitochondrial
KeywordsISOMERASE / cobalamin / mutase / vitamin B12
Function / homology
Function and homology information


succinyl-CoA biosynthetic process / Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / Propionyl-CoA catabolism / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / modified amino acid binding / homocysteine metabolic process ...succinyl-CoA biosynthetic process / Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / Propionyl-CoA catabolism / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / modified amino acid binding / homocysteine metabolic process / cobalamin binding / positive regulation of GTPase activity / post-embryonic development / mitochondrial matrix / GTPase activity / protein homodimerization activity / mitochondrion / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Methylmalonyl-CoA mutase signature. / 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 / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain
Similarity search - Domain/homology
COBALAMIN / Methylmalonyl-CoA mutase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMascarenhas, R.N. / Gouda, H. / Banerjee, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1-DK45776 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99-GM1434820 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Bivalent molecular mimicry by ADP protects metal redox state and promotes coenzyme B 12 repair.
Authors: Gouda, H. / Mascarenhas, R. / Ruetz, M. / Yaw, M. / Banerjee, R.
History
DepositionAug 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Methylmalonyl-CoA mutase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7198
Polymers84,8361
Non-polymers1,8837
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.377, 136.070, 196.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Methylmalonyl-CoA mutase, mitochondrial / MCM / Methylmalonyl-CoA isomerase


Mass: 84835.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMUT, MUT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22033, methylmalonyl-CoA mutase
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, pH 5.5, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.9→41.8 Å / Num. obs: 61448 / % possible obs: 98.4 % / Redundancy: 8.3 % / CC1/2: 1 / Net I/σ(I): 16.7
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 3258 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XIJ

2xij


Resolution: 1.9→39.763 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 3126 5.09 %
Rwork0.1745 58258 -
obs0.1763 61384 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.58 Å2 / Biso mean: 36.6386 Å2 / Biso min: 18.15 Å2
Refinement stepCycle: final / Resolution: 1.9→39.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 127 246 5656
Biso mean--35.46 36.82 -
Num. residues----703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92970.2608960.234214080
1.9297-1.96130.27321070.2313236687
1.9613-1.99520.24241300.2045240090
1.9952-2.03140.26511420.1919250594
2.0314-2.07050.23851240.1827262197
2.0705-2.11280.23081420.1846267499
2.1128-2.15870.23011730.18742654100
2.1587-2.20890.22161340.18112695100
2.2089-2.26420.23231440.17582687100
2.2642-2.32540.2251550.17712684100
2.3254-2.39380.22161410.16712710100
2.3938-2.4710.20781700.16922697100
2.471-2.55930.20431280.17062713100
2.5593-2.66180.23531350.17332703100
2.6618-2.78290.25231380.17972699100
2.7829-2.92960.22651340.18542721100
2.9296-3.11310.24061560.18452725100
3.1131-3.35330.20791550.18452713100
3.3533-3.69060.21131620.17292732100
3.6906-4.22410.19671430.15482747100
4.2241-5.31990.16751440.15432808100
5.3199-39.7630.1771730.1772864100
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)
10.246-0.0224-0.51111.5722-0.04761.64170.0894-0.04580.02830.01180.1293-0.3336-0.11080.3957-0.19870.2087-0.0024-0.05910.339-0.15670.3303-6.49290.61817.0781
22.09120.43380.2061.64720.26980.9525-0.09530.1499-0.55130.01460.1317-0.17860.04520.0252-0.03520.2659-0.0495-0.04150.2137-0.06610.3563-29.0157-26.008722.1343
30.93730.16790.04770.6281-0.54321.02970.0835-0.0122-0.1790.09030.0214-0.12180.09440.081-0.09810.2466-0.0014-0.07630.2342-0.0880.2979-15.6054-11.793715.3873
40.77080.1843-0.26430.7691-0.09150.67740.0858-0.1109-0.19530.19240.0073-0.05140.04780.0194-0.08080.2576-0.0044-0.08010.2494-0.04360.3053-23.1967-13.629322.0451
51.4309-0.4262-0.4082.66870.08131.89320.0144-0.0694-0.01230.33640.08170.2335-0.1267-0.41-0.08830.32620.0275-0.03020.3538-0.03470.1885-36.29145.69736.4135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 36 through 115 )B36 - 115
2X-RAY DIFFRACTION2chain 'B' and (resid 116 through 252 )B116 - 252
3X-RAY DIFFRACTION3chain 'B' and (resid 253 through 398 )B253 - 398
4X-RAY DIFFRACTION4chain 'B' and (resid 399 through 573 )B399 - 573
5X-RAY DIFFRACTION5chain 'B' and (resid 574 through 747 )B574 - 747

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