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PDBsum entry 1ccw

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1ccw
Jmol
Contents
Protein chains
137 a.a. *
483 a.a. *
Ligands
CNC ×2
TAR ×2
Waters ×1843
* Residue conservation analysis
PDB id:
1ccw
Name: Isomerase
Title: Structure of the coenzyme b12 dependent enzyme glutamate mut clostridium cochlearium
Structure: Protein (glutamate mutase). Chain: a, c. Fragment: b12-binding subunit. Synonym: methylaspartate mutase, component s. Engineered: yes. Other_details: chains a, c, b, d form heterotetramer which biological unit. Protein (glutamate mutase). Chain: b, d.
Source: Clostridium cochlearium. Organism_taxid: 1494. Atcc: dsm 1285. Collection: dsm 1285. Gene: glms. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: glme.
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.137     R-free:   0.173
Authors: R.Reitzer,K.Gruber,C.Kratky
Key ref:
R.Reitzer et al. (1999). Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights. Structure, 7, 891-902. PubMed id: 10467146 DOI: 10.1016/S0969-2126(99)80116-6
Date:
01-Mar-99     Release date:   01-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P80078  (MAMA_CLOCO) -  Glutamate mutase sigma subunit
Seq:
Struc:
137 a.a.
137 a.a.*
Protein chains
Pfam   ArchSchema ?
P80077  (GLME_CLOCO) -  Glutamate mutase epsilon subunit
Seq:
Struc:
483 a.a.
483 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.5.4.99.1  - Methylaspartate mutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-threo-3-methylaspartate = L-glutamate
L-threo-3-methylaspartate
Bound ligand (Het Group name = TAR)
matches with 66.67% similarity
= L-glutamate
      Cofactor: Cob(I)alamin
Cob(I)alamin
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(99)80116-6 Structure 7:891-902 (1999)
PubMed id: 10467146  
 
 
Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights.
R.Reitzer, K.Gruber, G.Jogl, U.G.Wagner, H.Bothe, W.Buckel, C.Kratky.
 
  ABSTRACT  
 
BACKGROUND: Glutamate mutase (Glm) equilibrates (S)-glutamate with (2S,3S)-3-methylaspartate. Catalysis proceeds with the homolytic cleavage of the organometallic bond of the cofactor to yield a 5'-desoxyadenosyl radical. This radical then abstracts a hydrogen atom from the protein-bound substrate to initiate the rearrangement reaction. Glm from Clostridium cochlearium is a heterotetrameric molecule consisting of two sigma and two epsilon polypeptide chains. RESULTS: We have determined the crystal structures of inactive recombinant Glm reconstituted with either cyanocobalamin or methylcobalamin. The molecule shows close similarity to the structure of methylmalonyl CoA mutase (MCM), despite poor sequence similarity between its catalytic epsilon subunit and the corresponding TIM-barrel domain of MCM. Each of the two independent B12 cofactor molecules is associated with a substrate-binding site, which was found to be occupied by a (2S,3S)-tartrate ion. A 1:1 mixture of cofactors with cobalt in oxidation states II and III was observed in both crystal structures of inactive Glm. CONCLUSIONS: The long axial cobalt-nitrogen bond first observed in the structure of MCM appears to result from a contribution of the species without upper ligand. The tight binding of the tartrate ion conforms to the requirements of tight control of the reactive intermediates and suggests how the enzyme might use the substrate-binding energy to initiate cleavage of the cobalt-carbon bond. The cofactor does not appear to have a participating role during the radical rearrangement reaction.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Ribbon representation of the epsilon, Greek [2]s[2](B[12])[2] tartrate[2] heterotetramer of Glm, viewed down the noncrystallographic dyad. The two epsilon, Greek subunits are coloured in red and green and the two s subunits are in yellow and blue. The B[12] cofactors are in cyan and the tartrate ions in magenta.
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 891-902) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20191656 E.N.Marsh, D.P.Patterson, and L.Li (2010).
Adenosyl radical: reagent and catalyst in enzyme reactions.
  Chembiochem, 11, 604-621.  
  20944207 M.D.Miller, L.Aravind, C.Bakolitsa, C.L.Rife, D.Carlton, P.Abdubek, T.Astakhova, H.L.Axelrod, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, J.Feuerhelm, J.C.Grant, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, H.van den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1167-1173.
PDB code: 3l5o
19328848 J.B.Weinberg, Y.Chen, N.Jiang, B.E.Beasley, J.C.Salerno, and D.K.Ghosh (2009).
Inhibition of nitric oxide synthase by cobalamins and cobinamides.
  Free Radic Biol Med, 46, 1626-1632.  
19236001 P.E.Mera, M.St Maurice, I.Rayment, and J.C.Escalante-Semerena (2009).
Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the activity of the enzyme.
  Biochemistry, 48, 3138-3145.
PDB codes: 3gah 3gai 3gaj
18953358 A.Chatterjee, Y.Li, Y.Zhang, T.L.Grove, M.Lee, C.Krebs, S.J.Booker, T.P.Begley, and S.E.Ealick (2008).
Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily.
  Nat Chem Biol, 4, 758-765.
PDB codes: 3epm 3epn 3epo
18506875 S.Gallo, M.Oberhuber, R.K.Sigel, and B.Kräutler (2008).
The corrin moiety of coenzyme B12 is the determinant for switching the btuB riboswitch of E. coli.
  Chembiochem, 9, 1408-1414.  
18586770 T.Toraya, N.Tamura, T.Watanabe, M.Yamanishi, N.Hieda, and K.Mori (2008).
Mechanism-based inactivation of coenzyme B12-dependent diol dehydratase by 3-unsaturated 1,2-diols and thioglycerol.
  J Biochem, 144, 437-446.  
17306212 A.Patwardhan, and E.N.Marsh (2007).
Changes in the free energy profile of glutamate mutase imparted by the mutation of an active site arginine residue to lysine.
  Arch Biochem Biophys, 461, 194-199.  
17407285 L.Hannibal, S.D.Bunge, R.van Eldik, D.W.Jacobsen, C.Kratky, K.Gruber, and N.E.Brasch (2007).
X-ray structural characterization of imidazolylcobalamin and histidinylcobalamin: cobalamin models for aquacobalamin bound to the B12 transporter protein transcobalamin.
  Inorg Chem, 46, 3613-3618.  
17171745 P.M.Kozlowski, T.Kamachi, T.Toraya, and K.Yoshizawa (2007).
Does Cob(II)alamin act as a conductor in coenzyme B12 dependent mutases?
  Angew Chem Int Ed Engl, 46, 980-983.  
16482346 K.L.Brown (2006).
The enzymatic activation of coenzyme B12.
  Dalton Trans, (), 1123-1133.  
16688781 L.Sun, and K.Warncke (2006).
Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a beta8alpha8, TIM-barrel fold and radical catalytic site structural features.
  Proteins, 64, 308-319.  
16981724 M.Yoon, A.Patwardhan, C.Qiao, S.O.Mansoorabadi, A.L.Menefee, G.H.Reed, and E.N.Marsh (2006).
Reaction of adenosylcobalamin-dependent glutamate mutase with 2-thiolglutarate.
  Biochemistry, 45, 11650-11657.  
16704345 W.Buckel, and B.T.Golding (2006).
Radical enzymes in anaerobes.
  Annu Rev Microbiol, 60, 27-49.  
16156797 M.Fukuoka, Y.Nakanishi, R.B.Hannak, B.Kräutler, and T.Toraya (2005).
Homoadenosylcobalamins as probes for exploring the active sites of coenzyme B12-dependent diol dehydratase and ethanolamine ammonia-lyase.
  FEBS J, 272, 4787-4796.  
15514022 F.Berkovitch, E.Behshad, K.H.Tang, E.A.Enns, P.A.Frey, and C.L.Drennan (2004).
A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.
  Proc Natl Acad Sci U S A, 101, 15870-15875.
PDB code: 1xrs
14704425 F.Berkovitch, Y.Nicolet, J.T.Wan, J.T.Jarrett, and C.L.Drennan (2004).
Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.
  Science, 303, 76-79.
PDB code: 1r30
  15374661 J.Kim, M.Hetzel, C.D.Boiangiu, and W.Buckel (2004).
Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of alpha-amino acids by anaerobic bacteria.
  FEMS Microbiol Rev, 28, 455-468.  
14675550 G.H.Reed, and S.O.Mansoorabadi (2003).
The positions of radical intermediates in the active sites of adenosylcobalamin-dependent enzymes.
  Curr Opin Struct Biol, 13, 716-721.  
12684496 N.Shibata, Y.Nakanishi, M.Fukuoka, M.Yamanishi, N.Yasuoka, and T.Toraya (2003).
Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase.
  J Biol Chem, 278, 22717-22725.
PDB codes: 1uc4 1uc5
14527323 R.Banerjee, and S.W.Ragsdale (2003).
The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes.
  Annu Rev Biochem, 72, 209-247.  
12029132 B.Hao, W.Gong, T.K.Ferguson, C.M.James, J.A.Krzycki, and M.K.Chan (2002).
A new UAG-encoded residue in the structure of a methanogen methyltransferase.
  Science, 296, 1462-1466.
PDB codes: 1l2q 1l2r 1nth
12413543 K.Gruber, and C.Kratky (2002).
Coenzyme B(12) dependent glutamate mutase.
  Curr Opin Chem Biol, 6, 598-603.  
11875520 M.D.Sintchak, G.Arjara, B.A.Kellogg, J.Stubbe, and C.L.Drennan (2002).
The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer.
  Nat Struct Biol, 9, 293-300.
PDB code: 1l1l
11893736 M.Vlasie, S.Chowdhury, and R.Banerjee (2002).
Importance of the histidine ligand to coenzyme B12 in the reaction catalyzed by methylmalonyl-CoA mutase.
  J Biol Chem, 277, 18523-18527.  
12230560 M.Yamanishi, M.Yunoki, T.Tobimatsu, H.Sato, J.Matsui, A.Dokiya, Y.Iuchi, K.Oe, K.Suto, N.Shibata, Y.Morimoto, N.Yasuoka, and T.Toraya (2002).
The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol.
  Eur J Biochem, 269, 4484-4494.
PDB code: 1iwp
12369058 T.Toraya (2002).
Enzymatic radical catalysis: coenzyme B12-dependent diol dehydratase.
  Chem Rec, 2, 352-366.  
11578922 E.N.Marsh, and C.L.Drennan (2001).
Adenosylcobalamin-dependent isomerases: new insights into structure and mechanism.
  Curr Opin Chem Biol, 5, 499-505.  
11592143 K.Gruber, R.Reitzer, and C.Kratky (2001).
Radical Shuttling in a Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer in the Coenzyme B(12) Dependent Enzyme Glutamate Mutase This work was supported by the Österreichische Akademie der Wissenschaften (APART fellowship 614), the Österreichische Fonds zur Förderung der wissenschaftlichen Forschung (FWF-project 11599), and the European Commission (TMR project number ERB 4061 PL 95-0307). Crystallographic data were collected at the EMBL-beamline BW7B at DESY in Hamburg, Germany. We thank the beamline scientists for their assistance, and Ingrid Dreveny, Günter Gartler, Gerwald Jogl, and Oliver Sauer for their help during data collection. This research emerged from a collaboration with Prof. W. Buckel (Marburg) who supplied us with clones of the glutamate mutase proteins.
  Angew Chem Int Ed Engl, 40, 3377-3380.
PDB code: 1i9c
11738186 P.M.Kozlowski (2001).
Quantum chemical modeling of Co--C bond activation in B(12)-dependent enzymes.
  Curr Opin Chem Biol, 5, 736-743.  
11755393 P.Madhavapeddi, and E.N.Marsh (2001).
The role of the active site glutamate in the rearrangement of glutamate to 3-methylaspartate catalyzed by adenosylcobalamin-dependent glutamate mutase.
  Chem Biol, 8, 1143-1149.  
10940017 B.Hoffmann, M.Oberhuber, E.Stupperich, H.Bothe, W.Buckel, R.Konrat, and B.Kräutler (2000).
Native corrinoids from Clostridium cochlearium are adeninylcobamides: spectroscopic analysis and identification of pseudovitamin B(12) and factor A.
  J Bacteriol, 182, 4773-4782.  
10903944 J.Masuda, N.Shibata, Y.Morimoto, T.Toraya, and N.Yasuoka (2000).
How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.
  Structure, 8, 775-788.
PDB codes: 1eex 1egm 1egv
10997901 T.Doukov, J.Seravalli, J.J.Stezowski, and S.W.Ragsdale (2000).
Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase.
  Structure, 8, 817-830.
PDB code: 1f6y
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.