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- PDB-8dyj: Crystal structure of human methylmalonyl-CoA mutase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8dyj
TitleCrystal structure of human methylmalonyl-CoA mutase in complex with ADP and cob(II)alamin
ComponentsMethylmalonyl-CoA mutase, mitochondrial
KeywordsISOMERASE / cobalamin / ADP / mutase / vitamin B12
Function / homology
Function and homology information


succinyl-CoA biosynthetic process / Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / Propionyl-CoA catabolism / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / 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 / Propionyl-CoA catabolism / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / modified amino acid binding / homocysteine metabolic process / cobalamin binding / post-embryonic development / positive regulation of GTPase activity / mitochondrial matrix / GTPase activity / protein homodimerization activity / mitochondrion / identical protein binding / metal ion 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
ADENOSINE-5'-DIPHOSPHATE / COBALAMIN / Methylmalonyl-CoA mutase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)86,5933
Polymers84,8361
Non-polymers1,7582
Water2,180121
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)61.025, 129.358, 188.422
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 / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M lithium sulfate monohydrate, 0.1 M sodium acetate trihydrate, 54% PEG 400

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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 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2.2→47.105 Å / Num. obs: 37982 / % possible obs: 99.2 % / Redundancy: 9 % / CC1/2: 0.99 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 3114 / CC1/2: 0.97

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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: 2XIQ

2xiq


Resolution: 2.2→47.105 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 1902 5.02 %
Rwork0.1949 36020 -
obs0.1964 37922 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.88 Å2 / Biso mean: 65.7701 Å2 / Biso min: 36.75 Å2
Refinement stepCycle: final / Resolution: 2.2→47.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 118 121 5651
Biso mean--52.41 54.11 -
Num. residues----708
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.25510.33241220.2739240694
2.2551-2.3160.31181280.2511253999
2.316-2.38420.27151250.24882579100
2.3842-2.46110.28871170.2364257099
2.4611-2.54910.27081400.2241258099
2.5491-2.65110.3061430.21682542100
2.6511-2.77180.24181330.22182561100
2.7718-2.91790.25771430.21992566100
2.9179-3.10070.27121420.23122589100
3.1007-3.340.24081650.2205249198
3.34-3.6760.23341260.19692616100
3.676-4.20770.17491320.17082652100
4.2077-5.30010.19971350.16222643100
5.3001-47.1050.20261510.1813268697
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)
10.67741.73650.81385.66361.37291.50240.1139-0.1122-0.10910.1862-0.34760.82470.349-0.63460.24010.5225-0.1240.18990.6671-0.13140.7554-4.0753-8.96137.3058
21.0364-0.28120.12931.64280.41111.90060.0373-0.12590.21380.2451-0.15570.2224-0.25710.03860.11910.4368-0.07070.06850.3773-0.03210.427615.08613.599417.1106
31.08780.5066-0.0885.75531.09272.60610.1302-0.27090.24310.4613-0.1278-0.0636-0.45230.353-0.03350.452-0.0748-0.08770.5690.02860.415327.885614.850827.5023
42.24470.1566-0.113.48160.83852.11720.0245-0.1237-0.06980.65690.1027-0.42120.53760.5928-0.11260.71380.0444-0.04410.6570.00420.325135.7647-6.796533.1209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 0 through 56 )B0 - 56
2X-RAY DIFFRACTION2chain 'B' and (resid 57 through 443 )B57 - 443
3X-RAY DIFFRACTION3chain 'B' and (resid 444 through 557 )B444 - 557
4X-RAY DIFFRACTION4chain 'B' and (resid 558 through 707 )B558 - 707

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