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- PDB-3bic: Crystal structure of human methylmalonyl-CoA mutase -

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Basic information

Entry
Database: PDB / ID: 3bic
TitleCrystal structure of human methylmalonyl-CoA mutase
ComponentsMethylmalonyl-CoA mutase, mitochondrial precursor
KeywordsISOMERASE / organic aciduria / methylmalonyl CoA mutase deficiency / metabolic disease / Structural Genomics / Structural Genomics Consortium / SGC / Cobalamin / Cobalt / Disease mutation / Metal-binding / Mitochondrion / Transit peptide
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 / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / 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-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / 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
Methylmalonyl-CoA mutase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsUgochukwu, E. / Kochan, G. / Pantic, N. / Parizotto, E. / Pilka, E.S. / Pike, A.C.W. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. ...Ugochukwu, E. / Kochan, G. / Pantic, N. / Parizotto, E. / Pilka, E.S. / Pike, A.C.W. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Oppermann, U. / Structural Genomics Consortium (SGC)
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.R. / Wu, X. / Gileadi, C. / Ugochukwu, E. / Krysztofinska, E. / Gravel, R.A. / Oppermann, U. / Yue, W.W.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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 precursor
B: Methylmalonyl-CoA mutase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,8136
Polymers169,6722
Non-polymers1424
Water1,51384
1
A: Methylmalonyl-CoA mutase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9073
Polymers84,8361
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methylmalonyl-CoA mutase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9073
Polymers84,8361
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.750, 95.150, 119.160
Angle α, β, γ (deg.)90.00, 108.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
12A
22B
32A
42B
52A
62B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROTRPTRP2AA38 - 32928 - 319
211PROPROTRPTRP2BB38 - 32928 - 319
321ILEILESERSER2AA333 - 594323 - 584
421ILEILESERSER2BB333 - 594323 - 584
531PROPROTHRTHR2AA615 - 673605 - 663
631PROPROTHRTHR2BB615 - 673605 - 663
741HISHISLYSLYS2AA678 - 745668 - 735
841HISHISLYSLYS2BB678 - 745668 - 735
112ALAALALEULEU6AA330 - 332320 - 322
212ALAALALEULEU6BB330 - 332320 - 322
322LYSLYSARGARG6AA595 - 614585 - 604
422LYSLYSARGARG6BB595 - 614585 - 604
532LEULEUGLYGLY6AA674 - 677664 - 667
632LEULEUGLYGLY6BB674 - 677664 - 667

NCS ensembles :
ID
1
2

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Components

#1: Protein Methylmalonyl-CoA mutase, mitochondrial precursor / / 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) / Gene: MUT / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P22033, methylmalonyl-CoA mutase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.60M Na/K2PO4, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97649 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97649 Å / Relative weight: 1
ReflectionResolution: 2.6→37.42 Å / Num. all: 67606 / Num. obs: 67606 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.698 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1REQ

1req


Resolution: 2.6→37.42 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / SU B: 20.894 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24341 1152 1.7 %RANDOM
Rwork0.21712 ---
all0.21758 66447 --
obs0.21758 66447 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å22.7 Å2
2---1.18 Å20 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10642 0 4 84 10730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210876
X-RAY DIFFRACTIONr_bond_other_d0.0020.027153
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9614786
X-RAY DIFFRACTIONr_angle_other_deg0.949317488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46151430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5124.283446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96151711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4011562
X-RAY DIFFRACTIONr_chiral_restr0.0610.21692
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022144
X-RAY DIFFRACTIONr_nbd_refined0.2070.22383
X-RAY DIFFRACTIONr_nbd_other0.1780.27230
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25440
X-RAY DIFFRACTIONr_nbtor_other0.0840.25610
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0180.21
X-RAY DIFFRACTIONr_mcbond_it0.4151.57282
X-RAY DIFFRACTIONr_mcbond_other0.0591.52906
X-RAY DIFFRACTIONr_mcangle_it0.701211337
X-RAY DIFFRACTIONr_scbond_it0.94734036
X-RAY DIFFRACTIONr_scangle_it1.5564.53446
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3949tight positional0.030.05
11A4260medium positional0.030.5
22B312loose positional0.575
11A3949tight thermal1.110
11A4260medium thermal1.1810
22B312loose thermal1.6210
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 53 -
Rwork0.343 4664 -
obs--94.6 %
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)
12.0538-0.0646-0.5320.5480.12850.6306-0.14070.3324-0.2991-0.0240.0333-0.19940.12470.11310.1074-0.0564-0.0353-0.0009-0.023-0.041-0.048-27.2312.9499-32.3537
21.05570.1099-0.14540.8789-0.00330.71810.02550.14120.19110.1003-0.02620.2765-0.1916-0.12760.0008-0.0327-0.03650.0174-0.1056-0.0089-0.073-64.881829.2415-20.18
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 74517 - 735
2X-RAY DIFFRACTION2BB38 - 75728 - 747

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