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- PDB-1e1c: METHYLMALONYL-COA MUTASE H244A Mutant -

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Basic information

Entry
Database: PDB / ID: 1e1c
TitleMETHYLMALONYL-COA MUTASE H244A Mutant
Components
  • METHYLMALONYL-COA MUTASE ALPHA CHAIN
  • METHYLMALONYL-COA MUTASE BETA CHAIN
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 (vitamin B12)-dependent enzyme, catalytic / Cobalamin-binding domain ...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 (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
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 / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsEvans, P.R. / Thoma, N.H.
CitationJournal: Biochemistry / Year: 2000
Title: Protection of Radical Intermediates at the Active Site of Adenosylcobalamin-Dependent Methylmalonyl-Coa Mutase
Authors: Thoma, N.H. / Evans, P.R. / Leadlay, P.F.
History
DepositionApr 30, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 ALPHA CHAIN
B: METHYLMALONYL-COA MUTASE BETA CHAIN
C: METHYLMALONYL-COA MUTASE ALPHA CHAIN
D: METHYLMALONYL-COA MUTASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,1348
Polymers299,0024
Non-polymers4,1324
Water27,4731525
1
A: METHYLMALONYL-COA MUTASE ALPHA CHAIN
B: METHYLMALONYL-COA MUTASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,5674
Polymers149,5012
Non-polymers2,0662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-86.4 kcal/mol
Surface area55000 Å2
MethodPQS
2
C: METHYLMALONYL-COA MUTASE ALPHA CHAIN
D: METHYLMALONYL-COA MUTASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,5674
Polymers149,5012
Non-polymers2,0662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-89.1 kcal/mol
Surface area55080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)125.398, 161.829, 166.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999851, 0.00324, -0.01696), (-0.003149, 0.99998, 0.005405), (0.016977, -0.005351, 0.999842)
Vector: 62.026, 0.196, -62.991)
DetailsBIOLOGICAL UNIT : HETERODIMERTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS TWOHETERODIMERIC MOLECULES , EACH WITH AN ALPHA CHAIN(CHAINS A AND C, CORRESPONDING TO GENE MUTB) AND A BETACHAIN ( CHAINS B AND D, CORRESPONDING TO GENE MUTA). MOLECULE 1 CONSISTS OF CHAINS A (ALPHA), B (BETA ), WITHWATERS X. MOLECULE 2 CONSISTS OF CHAINS C (ALPHA), D(BETA), WATERS Y. CHAINS A AND C INCLUDE COENZYME B12(RESIDUE 800), DESULPHO-COA ( RESIDUE 801)

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Components

#1: Protein METHYLMALONYL-COA MUTASE ALPHA CHAIN


Mass: 80070.781 Da / Num. of mol.: 2 / Fragment: WHOLE MOLECULE / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CHAINS A AND C INCLUDE COENZYME B12, AND DESULPHO-COA. B12 IS PRESENT LARGELY AS REDUCED COB(II)ALAMIN, OR B12R
Source: (gene. exp.) PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII (bacteria)
Strain: NCIB 9885 / Plasmid: PGP1-2, PMEX1 / Gene (production host): MUTA, MUTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K38 / References: UniProt: P11653, methylmalonyl-CoA mutase
#2: Protein METHYLMALONYL-COA MUTASE BETA CHAIN


Mass: 69430.188 Da / Num. of mol.: 2 / Fragment: WHOLE MOLECULE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII (bacteria)
Strain: NCIB 9885
Description: THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
Plasmid: PGP1-2, PMEX1 / Gene (production host): MUTA, MUTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K38 / References: UniProt: P11652, methylmalonyl-CoA mutase
#3: Chemical ChemComp-B12 / COBALAMIN


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1525 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A AND C ENGINEERED MUTATION HIS244ALA THIS STRUCTURE IS OF THE HIS244 - ALA MUTANT IN THE ...CHAIN A AND C ENGINEERED MUTATION HIS244ALA THIS STRUCTURE IS OF THE HIS244 - ALA MUTANT IN THE ALPHA CHAIN (A AND C). HIS244 IS A CATALYTIC RESIDUE HYDROGEN-BONDING TO THE CARBONYL GROUP OF THE SUBSTRATE: THIS MUTATION REDUCES KCAT BY ABOUT 1200-FOLD AND RENDERS THE ENZYME VERY SENSITIVE TO OXIDATION BY O2
Sequence detailsTHE SEQUENCES IN THE SWISSPROT DATABASE (MUTB, ALPHA CHAIN AND MUTA, ALPHA CHAIN) CONTAIN N- ...THE SEQUENCES IN THE SWISSPROT DATABASE (MUTB, ALPHA CHAIN AND MUTA, ALPHA CHAIN) CONTAIN N-TERMINAL METHIONINES WHICH ARE PROCESSED OFF THE EXPRESSED (AND WILD-TYPE) PROTEINS. THE EXPRESSED CHAINS ARE NUMBERED FROM RESIDUE 2. THE BETA CHAIN (MUTA) ALSO HAS 3 CORRECTIONS IN THE SEQUENCE COMPARED TO THE SWISSPROT DATABASE. 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).

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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: 2.83 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.5
Details: 14.4% PEG 4000, 20% V/V GLYCEROL, 12MM DESULPHO-COA, ADENOSYLCOBALAMIN 16MM,TRIS/HCL 100 MM, PH 7.5 THE CRYSTALS WERE GROWN IN THE PRESENCE OF 2MM EXCESS 5'-DEOXYADENOSYLCOBALAMIN (COENZYME ...Details: 14.4% PEG 4000, 20% V/V GLYCEROL, 12MM DESULPHO-COA, ADENOSYLCOBALAMIN 16MM,TRIS/HCL 100 MM, PH 7.5 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.
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop / Details: Mancia, F., (1999) Biochemitry, 38, 7999.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114.4 %PEG40001reservoir
220 %(v/v)glycerol1reservoir
312 mMdesulfo-CoA1reservoir
4100 mMTris-HCl1reservoir
516 mMAdoCbl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.62→29 Å / Num. obs: 335799 / % possible obs: 97.1 % / Observed criterion σ(I): 6 / Redundancy: 3.4 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 11.4
Reflection shellResolution: 2.62→2.76 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.446 / % possible all: 97.1
Reflection
*PLUS
Num. obs: 99776 / Num. measured all: 335799

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1REQ

1req


Resolution: 2.62→29.2 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 4167 4.2 %RANDOM
Rwork0.207 ---
obs0.219 99776 97.5 %-
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-4.9 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.62→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20506 0 276 1525 22307
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0570.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0640.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.93
X-RAY DIFFRACTIONp_mcangle_it4.75
X-RAY DIFFRACTIONp_scbond_it2.64
X-RAY DIFFRACTIONp_scangle_it6.86
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.20.15
X-RAY DIFFRACTIONp_singtor_nbd0.130.15
X-RAY DIFFRACTIONp_multtor_nbd0.190.15
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
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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