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- PDB-1req: METHYLMALONYL-COA MUTASE -

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Basic information

Entry
Database: PDB / ID: 1req
TitleMETHYLMALONYL-COA MUTASE
Components(METHYLMALONYL-COA ...) x 2
KeywordsISOMERASE / MUTASE / INTRAMOLECULAR TRANSFERASE
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 / metal ion binding / cytoplasm
Similarity search - Function
Methylmalonyl-CoA mutase small subunit, N-terminal / 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-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic ...Methylmalonyl-CoA mutase small subunit, N-terminal / 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-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
COBALAMIN / DESULFO-COENZYME A / Methylmalonyl-CoA mutase small subunit / Methylmalonyl-CoA mutase large subunit
Similarity search - Component
Biological speciesPropionibacterium freudenreichii subsp. shermanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsEvans, P.R. / Mancia, F.
Citation
Journal: Structure / Year: 1996
Title: How coenzyme B12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2 A resolution.
Authors: Mancia, F. / Keep, N.H. / Nakagawa, A. / Leadlay, P.F. / McSweeney, S. / Rasmussen, B. / Bosecke, P. / Diat, O. / Evans, P.R.
#1: Journal: Biochem.J. / Year: 1990
Title: Adenosylcobalamin-Dependent Methylmalonyl-Coa Mutase from Propionibacterium Shermanii. Active Holoenzyme Produced from Escherichia Coli
Authors: Mckie, N. / Keep, N.H. / Patchett, M.L. / Leadlay, P.F.
History
DepositionJan 19, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
B: METHYLMALONYL-COA MUTASE
C: METHYLMALONYL-COA MUTASE
D: METHYLMALONYL-COA MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,09717
Polymers299,1364
Non-polymers4,96013
Water27,5991532
1
A: METHYLMALONYL-COA MUTASE
B: METHYLMALONYL-COA MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,0949
Polymers149,5682
Non-polymers2,5267
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13090 Å2
ΔGint-56 kcal/mol
Surface area45370 Å2
MethodPISA
2
C: METHYLMALONYL-COA MUTASE
D: METHYLMALONYL-COA MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,0028
Polymers149,5682
Non-polymers2,4346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-56 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.800, 161.300, 88.400
Angle α, β, γ (deg.)90.00, 105.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.464135, 0.013887, 0.885656), (-0.012319, -0.999882, 0.009222), (0.885679, -0.00663, 0.464251)
Vector: 15.3186, 161.30537, -9.0062)
DetailsTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS TWO HETERODIMERIC MOLECULES, EACH WITH AN ALPHA CHAIN (CHAINS A AND C, CORRESPONDING TO GENE MUTB) AND A BETA CHAIN (CHAINS B AND D, CORRESPONDING TO GENE MUTA). MOLECULE 1 CONSISTS OF CHAINS A (ALPHA), B (BETA), WITH GLYCEROL CHAIN G AND WATERS X. MOLECULE 2 CONSISTS OF CHAINS C (ALPHA), D (BETA), WITH GLYCEROL CHAIN H AND WATERS Y. CHAINS A AND C INCLUDE COENZYME B12 (RESIDUE 800), DESULPHO-COA (RESIDUE 801) AND A GLYCEROL IN THE ACTIVE SITE (RESIDUE 802).

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Components

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METHYLMALONYL-COA ... , 2 types, 4 molecules ACBD

#1: Protein METHYLMALONYL-COA MUTASE /


Mass: 80137.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHAINS A AND C INCLUDE COENZYME B12, DESULPHO-COA, AND A GLYCEROL IN THE ACTIVE SITE. B12 IS PRESENT LARGELY AS REDUCED COB(II)ALAMIN, OR B12R.
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: NCIB 9885
Description: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
Cell line: 293 / Gene: MUTA MUTB / Plasmid: PMEX1 / Gene (production host): MUTA, MUTB / Production host: K38 PGP1-2 / Strain (production host): 293 / References: UniProt: P11653, methylmalonyl-CoA mutase
#2: Protein METHYLMALONYL-COA MUTASE /


Mass: 69430.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHAINS A AND C INCLUDE COENZYME B12, DESULPHO-COA, AND A GLYCEROL IN THE ACTIVE SITE. B12 IS PRESENT LARGELY AS REDUCED COB(II)ALAMIN, OR B12R.
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: NCIB 9885
Description: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
Cell line: 293 / Gene: MUTA MUTB / Plasmid: PMEX1 / Gene (production host): MUTA, MUTB / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P11652, methylmalonyl-CoA mutase

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Non-polymers , 4 types, 1545 molecules

#3: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical ChemComp-DCA / DESULFO-COENZYME A


Mass: 735.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1532 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 48 %
Crystal growDetails: THE CRYSTALS WERE GROWN IN THE PRESENCE OF 2MM EXCESS 5'-DEOXYADENOSYLCOBALAMIN (COENZYME B12) AND 12MM DESULPHO-COA (FINAL CONCENTRATIONS), EQUILIBRATED AGAINST 14% W/V PEG 4000 AND 20% V/V ...Details: THE CRYSTALS WERE GROWN IN THE PRESENCE OF 2MM EXCESS 5'-DEOXYADENOSYLCOBALAMIN (COENZYME B12) AND 12MM DESULPHO-COA (FINAL CONCENTRATIONS), EQUILIBRATED AGAINST 14% W/V PEG 4000 AND 20% V/V GLYCEROL, 100MM TRIS PH 7.5. THE ELECTRON DENSITY MAPS SHOW NO ADENOSYL GROUP ATTACHED TO THE COBALT ATOM, AND SPECTRA FROM SIMILAR CRYSTALS SHOW EVIDENCE OF SUBSTANTIAL REDUCTION OF COIII TO COII, WHICH IS 5-COORDINATE. THE COBALAMIN IN THIS CRYSTAL STRUCTURE IS BEST CONSIDERED AS REDUCED COB(II)ALAMIN (OR B12R). THE BOND LENGTH FROM THE COBALT TO THE LOWER AXIAL LIGAND, NE2 OF HIS A 610 (OR HIS C 610) IS SIGNIFICANTLY LONGER THAN THAT IN MODEL COMPOUNDS. POORLY ORDERED LOOPS: DENSITY IN THE FOLLOWING REGIONS IS POOR, AND THE MODEL MUST BE CONSIDERED UNRELIABLE. ALPHA CHAIN: A 1, C 1 MISSING, A 2 - A 3, C 2 - C 3 WEAK. BETA CHAIN: B 1 - C 19, C 1 - C 16 MISSING; B 184 - B 191, D 184 - D 191 WEAK; D 228 - D 230 WEAK; D 271 - D 276 VERY POOR DENSITY (MUCH BETTER IN CHAIN B); D 315 WEAK; D 474 - D 428 WEAK.
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %(w/v)PEG40001reservoir
220 %(v/v)glycerol1reservoir
3100 mMTris-HCl1reservoir
414 %(w/v)PEG40001drop
520 %(v/v)glycerol1drop
6100 mMTris-HCl1drop
720 mg/mlprotein1drop
82 mMcoenzyme B121drop
912 mMdesulpho-CoA1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 217377 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 4.6 % / Rmerge(I) obs: 0.051
Reflection
*PLUS
Num. measured all: 1008268

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
RefinementResolution: 2→20 Å / σ(F): 0
Details: DERIVED FROM ENGH AND HUBER PARAMETERS BY V. LAMZIN FINAL RMS COORD. SHIFT 0.009 ANGSTROMS
RfactorNum. reflection% reflection
Rfree0.275 10907 5 %
Rwork0.22 --
obs-206327 99.8 %
Displacement parametersBiso mean: 42 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20510 0 330 1532 22372
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.23
X-RAY DIFFRACTIONp_mcangle_it4.15
X-RAY DIFFRACTIONp_scbond_it4.64
X-RAY DIFFRACTIONp_scangle_it5.86
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1560.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1870.3
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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