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- PDB-4req: Methylmalonyl-COA Mutase substrate complex -

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Basic information

Entry
Database: PDB / ID: 4req
TitleMethylmalonyl-COA Mutase substrate complex
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
5'-DEOXYADENOSINE / COBALAMIN / METHYLMALONYL-COENZYME A / SUCCINYL-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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEvans, P.R. / Mancia, F.
Citation
Journal: Structure / Year: 1998
Title: Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism.
Authors: Mancia, F. / Evans, P.R.
#1: Journal: Vitamin B12 and B12-Proteins : Lectures Presented at the 4Th European Symposium on Vitamin B12 and B12-Proteins
Year: 1998
Title: Insights on the Reaction Mechanism of Methylmalonyl-Coa Mutase from the Crystal Structure
Authors: Evans, P.R. / Mancia, F.
History
DepositionJun 17, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)306,13816
Polymers299,1364
Non-polymers7,00212
Water23,1671286
1
A: METHYLMALONYL-COA MUTASE
B: METHYLMALONYL-COA MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,0698
Polymers149,5682
Non-polymers3,5016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-82 kcal/mol
Surface area45480 Å2
MethodPISA
2
C: METHYLMALONYL-COA MUTASE
D: METHYLMALONYL-COA MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,0698
Polymers149,5682
Non-polymers3,5016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14280 Å2
ΔGint-81 kcal/mol
Surface area45350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.130, 160.900, 88.500
Angle α, β, γ (deg.)90.00, 104.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.462866, -0.001054, 0.886428), (-0.000176, -0.999999, -0.001281), (0.886428, -0.000749, 0.462865)
Vector: 17.227, 161.68442, -9.96059)
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), A 1:1 MIXTURE OF SUBSTRATE AND PRODUCT, SUCCINYL-COA (RESIDUE 801), METHYLMALONYL-COA (RESIDUE 802), AND A HALF-OCCUPIED 5'-DEOXYADENOSINE INTERMEDIATE.

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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 natural source
Details: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
Source: (natural) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Plasmid: PMEX1 / Species: Propionibacterium freudenreichii / Strain: NCIB 9885 / References: UniProt: P11653, methylmalonyl-CoA mutase
#2: Protein METHYLMALONYL-COA MUTASE /


Mass: 69430.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
Source: (natural) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Plasmid: PMEX1 / Species: Propionibacterium freudenreichii / Strain: NCIB 9885 / References: UniProt: P11652, methylmalonyl-CoA mutase

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Non-polymers , 6 types, 1298 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-SCA / SUCCINYL-COENZYME A / Succinyl-CoA


Mass: 867.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O19P3S
#5: Chemical ChemComp-MCA / METHYLMALONYL-COENZYME A / Methylmalonyl-CoA


Mass: 867.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O19P3S
#6: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 1286 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS ...THE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS NO ELECTRON DENSITY FOR AN ADENOSYL GROUP LINKED TO THE COBALT ATOM. HOWEVER, A HALF-OCCUPIED 5'-DEOXYADENOSINE HAS BEEN BUILT INTO ELECTRON DENSITY IN THE ACTIVE SITE (RESIDUES A803 AND AND C803). RESIDUES A801 AND A802 (AND C801, C802) REPRESENT AN EQUIMOLAR MIXTURE OF SUBSTRATE AND PRODUCT, SUCCINYL- AND METHYLMALONYL-COENZYME A.

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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: 2.74 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.24
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Sep 1, 1995 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 164181 / % possible obs: 99.8 % / Observed criterion σ(I): 3.5 / Redundancy: 4.3 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 5.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.379 / % possible all: 99.9

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1REQ

1req


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 7570 5 %RANDOM
Rwork0.222 ---
obs0.232 164053 99.9 %-
Displacement parametersBiso mean: 38 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20586 0 462 1286 22334
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.23
X-RAY DIFFRACTIONp_mcangle_it3.25
X-RAY DIFFRACTIONp_scbond_it3.34
X-RAY DIFFRACTIONp_scangle_it4.56
X-RAY DIFFRACTIONp_plane_restr0.0040.02
X-RAY DIFFRACTIONp_chiral_restr0.1470.15
X-RAY DIFFRACTIONp_singtor_nbd0.1290.15
X-RAY DIFFRACTIONp_multtor_nbd0.1780.15
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1250.15
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

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