DB code: T00236

CATH domain 3.20.20.240 : TIM Barrel Catalytic domain
3.90.970.10 : Glutamate mutase, C-terminal domain
3.40.50.280 : Rossmann fold Catalytic domain
E.C. 5.4.99.1
CSA 1cb7
M-CSA 1cb7
MACiE M0063

CATH domain Related DB codes (homologues)
3.20.20.240 : TIM Barrel M00168
3.40.50.280 : Rossmann fold M00172 M00168

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P80077 Methylaspartate mutase E chain
EC 5.4.99.1
Glutamate mutase subunit epsilon
PF06368 (Met_asp_mut_E)
[Graphical View]
P80078 Methylaspartate mutase S chain
EC 5.4.99.1
Glutamate mutase subunit sigma
PF02310 (B12-binding)
[Graphical View]
Q05509 Methylaspartate mutase E chain
EC 5.4.99.1
Glutamate mutase subunit epsilon
PF06368 (Met_asp_mut_E)
[Graphical View]
Q05488 Methylaspartate mutase S chain
EC 5.4.99.1
Glutamate mutase subunit sigma
PF02310 (B12-binding)
[Graphical View]

KEGG enzyme name
methylaspartate mutase
glutamate mutase
glutamic mutase
glutamic isomerase
glutamic acid mutase
glutamic acid isomerase
methylaspartic acid mutase
beta-methylaspartate-glutamate mutase
glutamate isomerase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P80077 GLME_CLOCO L-threo-3-methylaspartate = L-glutamate. Heterotetramer of 2 E subunits and 2 S subunits. Cobalamin.
P80078 MAMA_CLOCO L-threo-3-methylaspartate = L-glutamate. Heterotetramer of 2 E subunits and 2 S subunits. 5''-deoxy-5''-adenosyl-adeninylcobamide (pseudo-coenzyme B12).
Q05509 GLME_CLOTT L-threo-3-methylaspartate = L-glutamate. Possible heterotetramer, composed of two E chains and two S chains. E exists as a homodimer and S as a monomer. Cobalamin.
Q05488 MAMA_CLOTT L-threo-3-methylaspartate = L-glutamate. Heterotetramer of 2 E subunits and 2 S subunits. E exists as a homodimer and S as a monomer. 5''-deoxy-5''-adenosyl-adeninylcobamide (pseudo-coenzyme B12).

KEGG Pathways
Map code Pathways E.C.
MAP00660 C5-Branched dibasic acid metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00194 C03618 C00025
E.C.
Compound Cobamide coenzyme L-threo-3-Methylaspartate L-Glutamate
Type amide group,amine group,aromatic ring (with nitrogen atoms),carbohydrate,heavy metal,nucleoside,nucleotide amino acids,carboxyl group amino acids,carboxyl group
ChEBI 47980
16015
PubChem 440064
33032
44272391
88747398
1cb7B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:TAR Unbound
1cb7D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:TAR Unbound
1ccwB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:TAR Unbound
1ccwD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:TAR Unbound
1i9cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:5AD Bound:3MD Bound:GLU
1i9cD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:5AD Bound:3MD Bound:GLU
1cb7B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1cb7D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1ccwB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1ccwD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1i9cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1i9cD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1b1aA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1cb7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:COB Unbound Unbound
1cb7C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:COB Unbound Unbound
1ccwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CNC Unbound Unbound
1ccwC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:CNC Unbound Unbound
1i9cA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:B12 Unbound Unbound
1i9cC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:B12 Unbound Unbound
1be1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1fmfA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1id8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [14], [18], [28]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1cb7B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 100;GLU 171
1cb7D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 100;GLU 171
1ccwB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 100;GLU 171
1ccwD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 100;GLU 171
1i9cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 100;GLU 171
1i9cD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 100;GLU 171
1cb7B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1cb7D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ccwB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ccwD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1i9cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1i9cD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1b1aA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)
1cb7A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)
1cb7C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)
1ccwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)
1ccwC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)
1i9cA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)
1i9cC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)
1be1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)
1fmfA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)
1id8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 14 HIS 16(Cobamide coenzyme binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[9]
Scheme 1, Scheme 2
[10]
Fig.2, p.11870-11872
[12]
Fig.1
[14]
Fig.1, p.897, p.899-900
[15]
Fig.5
[16]
Scheme 2
[17]
Scheme 1
[18]
Fig. 1, Fig.5, p.1147-1148
[20]
[25]
Fig.4, p.600-601
[26]
[28]
Fig.1, p.3243-3245
[29]
Fig.1, Fig.4, p.2690-2691

References
[1]
Resource
Comments
Medline ID
PubMed ID 1315276
Journal Eur J Biochem
Year 1992
Volume 205
Pages 759-65
Authors Leutbecher U, Bocher R, Linder D, Buckel W
Title Glutamate mutase from Clostridium cochlearium. Purification, cobamide content and stereospecific inhibitors.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1322827
Journal FEBS Lett
Year 1992
Volume 307
Pages 144-6
Authors Leutbecher U, Albracht SP, Buckel W
Title Identification of a paramagnetic species as an early intermediate in the coenzyme B12-dependent glutamate mutase reaction. A cob(II)amide?
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7712296
Journal Curr Opin Struct Biol
Year 1994
Volume 4
Pages 919-29
Authors Drennan CL, Matthews RG, Ludwig ML
Title Cobalamin-dependent methionine synthase: the structure of a methylcobalamin-binding fragment and implications for other B12-dependent enzymes.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7880251
Journal Eur J Biochem
Year 1994
Volume 226
Pages 577-85
Authors Zelder O, Beatrix B, Leutbecher U, Buckel W
Title Characterization of the coenzyme-B12-dependent glutamate mutase from Clostridium cochlearium produced in Escherichia coli.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7649266
Journal FEBS Lett
Year 1995
Volume 369
Pages 252-4
Authors Zelder O, Beatrix B, Kroll F, Buckel W
Title Coordination of a histidine residue of the protein-component S to the cobalt atom in coenzyme B12-dependent glutamate mutase from Clostridium cochlearium.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9003368
Journal Biochem J
Year 1996
Volume 320
Pages 825-30
Authors Holloway DE, Harding SE, Marsh EN
Title Adenosylcobalamin-dependent glutamate mutase: properties of a fusion protein in which the cobalamin-binding subunit is linked to the catalytic subunit.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 8910568
Journal J Biol Chem
Year 1996
Volume 271
Pages 29121-5
Authors Holloway DE, Chen HP, Marsh EN
Title Carboxymethylation of MutS-cysteine-15 specifically inactivates adenosylcobalamin-dependent glutamate mutase. Examination of the role of this residue in coenzyme-binding and catalysis.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9201933
Journal Biochemistry
Year 1997
Volume 36
Pages 7884-9
Authors Chen HP, Marsh EN
Title How enzymes control the reactivity of adenosylcobalamin: effect on coenzyme binding and catalysis of mutations in the conserved histidine-aspartate pair of glutamate mutase.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9521732
Journal Biochemistry
Year 1998
Volume 37
Pages 4105-13
Authors Bothe H, Darley DJ, Albracht SP, Gerfen GJ, Golding BT, Buckel W
Title Identification of the 4-glutamyl radical as an intermediate in the carbon skeleton rearrangement catalyzed by coenzyme B12-dependent glutamate mutase from Clostridium cochlearium.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9718309
Journal Biochemistry
Year 1998
Volume 37
Pages 11864-72
Authors Marsh EN, Ballou DP
Title Coupling of cobalt-carbon bond homolysis and hydrogen atom abstraction in adenosylcobalamin-dependent glutamate mutase.
Related PDB
Related UniProtKB
[11]
Resource
Comments STRUCTURE BY NMR.
Medline ID
PubMed ID 9739092
Journal Structure
Year 1998
Volume 6
Pages 1021-33
Authors Tollinger M, Konrat R, Hilbert BH, Marsh EN, Krautler B
Title How a protein prepares for B12 binding: structure and dynamics of the B12-binding subunit of glutamate mutase from Clostridium tetanomorphum.
Related PDB 1be1
Related UniProtKB Q05488
[12]
Resource
Comments
Medline ID
PubMed ID 10521275
Journal Biochemistry
Year 1999
Volume 38
Pages 13684-91
Authors Chih HW, Marsh EN
Title Pre-steady-state kinetic investigation of intermediates in the reaction catalyzed by adenosylcobalamin-dependent glutamate mutase.
Related PDB
Related UniProtKB
[13]
Resource
Comments NMR spectroscopy
Medline ID
PubMed ID 10429202
Journal Eur J Biochem
Year 1999
Volume 263
Pages 178-88
Authors Hoffmann B, Konrat R, Bothe H, Buckel W, Krautler B
Title Structure and dynamics of the B12-binding subunit of glutamate mutase from Clostridium cochlearium.
Related PDB 1b1a
Related UniProtKB
[14]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID 99404935
PubMed ID 10467146
Journal Structure Fold Des
Year 1999
Volume 7
Pages 891-902
Authors Reitzer R, Gruber K, Jogl G, Wagner UG, Bothe H, Buckel W, Kratky C
Title Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights.
Related PDB 1cb7 1ccw
Related UniProtKB P80077
[15]
Resource
Comments
Medline ID
PubMed ID 10956023
Journal Biochemistry
Year 2000
Volume 39
Pages 10340-6
Authors Roymoulik I, Moon N, Dunham WR, Ballou DP, Marsh EN
Title Rearrangement of L-2-hydroxyglutarate to L-threo-3-methylmalate catalyzed by adenosylcobalamin-dependent glutamate mutase.
Related PDB
Related UniProtKB
[16]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11592143
Journal Angew Chem Int Ed Engl
Year 2001
Volume 40
Pages 3377-3380
Authors Gruber K, Reitzer R, Kratky C
Title Radical Shuttling in a Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer in the Coenzyme B(12) Dependent Enzyme Glutamate Mutase.
Related PDB 1i9c
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11256957
Journal Biochem J
Year 2001
Volume 355
Pages 131-7
Authors Huhta MS, Chen HP, Hemann C, Hille CR, Marsh EN
Title Protein-coenzyme interactions in adenosylcobalamin-dependent glutamate mutase.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11755393
Journal Chem Biol
Year 2001
Volume 8
Pages 1143-9
Authors Madhavapeddi P, Marsh EN
Title The role of the active site glutamate in the rearrangement of glutamate to 3-methylaspartate catalyzed by adenosylcobalamin-dependent glutamate mutase.
Related PDB
Related UniProtKB
[19]
Resource
Comments NMR spectroscopy
Medline ID
PubMed ID 11828501
Journal Chembiochem
Year 2001
Volume 2
Pages 643-55
Authors Hoffmann B, Tollinger M, Konrat R, Huhta M, Marsh EN, Krautler B
Title A protein pre-organized to trap the nucleotide moiety of coenzyme B(12): refined solution structure of the B(12)-binding subunit of glutamate mutase from Clostridium tetanomorphum.
Related PDB 1fmf
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11506551
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 7963-72
Authors Wetmore SD, Smith DM, Golding BT, Radom L
Title Interconversion of (S)-glutamate and (2S,3S)-3-methylaspartate: a distinctive B(12)-dependent carbon-skeleton rearrangement.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11727974
Journal J Biomol NMR
Year 2001
Volume 21
Pages 107-16
Authors Eichmuller C, Schuler W, Konrat R, Krautler B
Title Simultaneous measurement of intra- and intermolecular NOEs in differentially labeled protein-ligand complexes.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 11519744
Journal J Biomol NMR
Year 2001
Volume 20
Pages 195-202
Authors Eichmuller C, Tollinger M, Krautler B, Konrat R
Title Mapping the ligand binding site at protein side-chains in protein-ligand complexes through NOE difference spectroscopy.
Related PDB
Related UniProtKB
[23]
Resource
Comments NMR spectroscopy
Medline ID
PubMed ID 11397096
Journal J Mol Biol
Year 2001
Volume 309
Pages 777-91
Authors Tollinger M, Eichmuller C, Konrat R, Huhta MS, Marsh EN, Krautler B
Title The B(12)-binding subunit of glutamate mutase from Clostridium tetanomorphum traps the nucleotide moiety of coenzyme B(12).
Related PDB 1id8
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 11863459
Journal Biochemistry
Year 2002
Volume 41
Pages 3200-6
Authors Huhta MS, Ciceri D, Golding BT, Marsh EN
Title A novel reaction between adenosylcobalamin and 2-methyleneglutarate catalyzed by glutamate mutase.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 12413543
Journal Curr Opin Chem Biol
Year 2002
Volume 6
Pages 598-603
Authors Gruber K, Kratky C
Title Coenzyme B(12) dependent glutamate mutase.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 12797824
Journal Chem Rev
Year 2003
Volume 103
Pages 2083-94
Authors Banerjee R
Title Radical carbon skeleton rearrangements: catalysis by coenzyme B12-dependent mutases.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 14979711
Journal Biochemistry
Year 2004
Volume 43
Pages 2155-8
Authors Cheng MC, Marsh EN
Title Pre-steady-state measurement of intrinsic secondary tritium isotope effects associated with the homolysis of adenosylcobalamin and the formation of 5'-deoxyadensosine in glutamate mutase.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 15023074
Journal Biochemistry
Year 2004
Volume 43
Pages 3238-45
Authors Xia L, Ballou DP, Marsh EN
Title Role of Arg100 in the active site of adenosylcobalamin-dependent glutamate mutase.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 15709782
Journal Biochemistry
Year 2005
Volume 44
Pages 2686-91
Authors Cheng MC, Marsh EN
Title Isotope effects for deuterium transfer between substrate and coenzyme in adenosylcobalamin-dependent glutamate mutase.
Related PDB
Related UniProtKB

Comments
According to the literature, this enzyme catalyzes "fragmentation" and "recombination" by radical transfer from Cobamide coenzyme (or Vitamine B12).

Created Updated
2005-05-20 2009-03-10