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- PDB-2xiq: Crystal structure of human methylmalonyl-CoA mutase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2xiq
TitleCrystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin and malonyl-CoA
ComponentsMETHYLMALONYL-COA MUTASE, MITOCHONDRIAL
KeywordsISOMERASE / ORGANIC ACIDURIA / METABOLIC DISEASE / 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 / 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 ...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 / MALONYL-COENZYME A / Methylmalonyl-CoA mutase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYue, W.W. / Froese, D.S. / Kochan, G. / Chaikuad, A. / Krojer, T. / Muniz, J. / Ugochukwu, E. / Arrowsmith, C. / Weigelt, J. / Edwards, A. ...Yue, W.W. / Froese, D.S. / Kochan, G. / Chaikuad, A. / Krojer, T. / Muniz, J. / Ugochukwu, E. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structures of the Human Gtpase Mmaa and Vitamin B12-Dependent Methylmalonyl-Coa Mutase and Insight Into Their Complex Formation.
Authors: Froese, D.S. / Kochan, G. / Muniz, J. / Wu, X. / Gileadi, C. / Ugochukwu, E. / Krysztofinska, E. / Gravel, R.A. / Oppermann, U. / Yue, W.W.
History
DepositionJun 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Derived calculations / Refinement description / Version format compliance
Revision 1.2Oct 31, 2012Group: Non-polymer description
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: database_PDB_caveat / pdbx_database_status ...database_PDB_caveat / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: METHYLMALONYL-COA MUTASE, MITOCHONDRIAL
B: METHYLMALONYL-COA MUTASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,5428
Polymers169,6722
Non-polymers4,8706
Water19,9251106
1
A: METHYLMALONYL-COA MUTASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2714
Polymers84,8361
Non-polymers2,4353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: METHYLMALONYL-COA MUTASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2714
Polymers84,8361
Non-polymers2,4353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: METHYLMALONYL-COA MUTASE, MITOCHONDRIAL
hetero molecules

B: METHYLMALONYL-COA MUTASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,5428
Polymers169,6722
Non-polymers4,8706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Buried area15910 Å2
ΔGint-81.2 kcal/mol
Surface area47590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.650, 143.620, 163.230
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, MITOCHONDRIAL / MCM / METHYLMALONYL-COA ISOMERASE


Mass: 84835.820 Da / Num. of mol.: 2 / Fragment: RESIDUES 12-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3-PRARE2 / References: UniProt: P22033, methylmalonyl-CoA mutase
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#4: Chemical ChemComp-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H38N7O19P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1106 / 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: 2.75 Å3/Da / Density % sol: 55.3 % / Description: NONE
Crystal growDetails: 20% PEG3350, 0.1 M BIS-TRIS PH 5.5, 0.1 M NH4-SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9824
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2010
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9824 Å / Relative weight: 1
ReflectionResolution: 1.95→53.91 Å / Num. obs: 129983 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BIC

3bic


Resolution: 1.95→107.82 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.371 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.133 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 6447 5 %RANDOM
Rwork0.16106 ---
obs0.16306 122461 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.705 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å20 Å2
2---0.47 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→107.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11009 0 326 1106 12441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5772.00715853
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00351435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44524.194496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98151979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0051579
X-RAY DIFFRACTIONr_chiral_restr0.0770.21762
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218743
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 405 -
Rwork0.311 8628 -
obs--94.99 %
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)
11.4154-0.1350.44975.05540.76041.9735-0.08850.1428-0.0935-0.36510.1818-0.7948-0.0740.4448-0.09330.175-0.07330.08380.19230.00380.158342.54171.848129.634
20.7038-0.07090.4141.1168-0.13411.236-0.06730.03280.1131-0.06620.0389-0.0403-0.48170.02230.02840.349-0.01350.01140.06320.02810.030422.32591.506125.917
32.4215-3.9626-0.53449.4889-0.48012.2005-0.3887-0.0703-0.26950.54130.390.7365-0.1444-0.4328-0.00140.20970.054-0.02550.26030.05420.09115.10777.452122.93
42.7792-0.7804-0.52222.562-0.20133.764-0.1134-0.10670.4434-0.3367-0.03830.2883-0.8506-0.27790.15170.87940.1222-0.09920.15680.02250.21839.711112.897116.211
57.75820.33562.80642.18910.73116.0877-0.1167-0.0292-0.49780.11870.14110.19970.0306-0.1668-0.02440.1522-0.00420.02080.11220.03130.059912.66966.79797.62
61.5953-0.89420.3911.5694-0.38522.4433-0.0477-0.008-0.08150.1130.09240.204-0.1175-0.357-0.04470.19260.03550.0050.15430.05810.04981.47378.118105.95
71.2477-0.3054-0.09534.417-0.90832.7329-0.0697-0.0429-0.21720.16380.13830.67010.5277-0.411-0.06860.1542-0.07290.03550.16620.00450.1304-4.43868.28263.5
80.68950.26220.05091.10860.07230.99180.0221-0.00830.08780.07620.01720.0925-0.0354-0.0266-0.03940.0457-0.00220.01360.05570.0130.020313.1189.56567.565
91.72161.1578-0.277524.72373.40160.85020.03430.0756-0.0299-0.5140.0197-0.6848-0.07460.0939-0.0540.1823-0.0546-0.04410.31850.01730.103338.19994.04868.419
102.0291.8036-1.07223.2294-1.15633.42450.0503-0.24090.35240.5115-0.2910.0473-0.32410.07170.24080.2915-0.0352-0.03350.0714-0.04030.193220.672113.71577.614
116.961.7213.14772.6961-0.09166.05810.1486-0.1116-0.34290.00670.1062-0.3060.26420.2142-0.25470.15920.02580.00960.13560.00840.056825.74967.72595.651
120.5980.47070.01971.7529-0.8781.68930.0382-0.0853-0.05670.1987-0.0785-0.3465-0.05020.42120.04030.1242-0.0128-0.04640.236-0.01960.10535.21880.64987.368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 103
2X-RAY DIFFRACTION2A104 - 477
3X-RAY DIFFRACTION3A478 - 518
4X-RAY DIFFRACTION4A519 - 579
5X-RAY DIFFRACTION5A580 - 616
6X-RAY DIFFRACTION6A617 - 747
7X-RAY DIFFRACTION7B36 - 103
8X-RAY DIFFRACTION8B104 - 494
9X-RAY DIFFRACTION9B495 - 522
10X-RAY DIFFRACTION10B523 - 579
11X-RAY DIFFRACTION11B580 - 616
12X-RAY DIFFRACTION12B617 - 747

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