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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ZN(II)-BOUND GLYOXALASE I OF ESCHERICHIA COLI
 
Authors :  M. M. He, S. L. Clugston, J. F. Honek, B. W. Matthews
Date :  12 Jul 00  (Deposition) - 20 Sep 00  (Release) - 18 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha-Beta-Beta-Beta Motif, Homodimer, Zn(Ii)-Bound, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. He, S. L. Clugston, J. F. Honek, B. W. Matthews
Determination Of The Structure Of Escherichia Coli Glyoxalase I Suggests A Structural Basis For Differential Metal Activation.
Biochemistry V. 39 8719 2000
PubMed-ID: 10913283  |  Reference-DOI: 10.1021/BI000856G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYOXALASE I
    Chains: A, B
    EC Number: 4.4.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: LACTOYLGLUTATHIONE LYASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:5 , GLU A:56 , HIS B:74 , GLU B:122 , HOH B:216BINDING SITE FOR RESIDUE ZN A 1200
2AC2SOFTWAREHIS A:74 , GLU A:122 , HIS B:5 , GLU B:56 , HOH B:204BINDING SITE FOR RESIDUE ZN A 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FA5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FA5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FA5)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VOCPS51819 Vicinal oxygen chelate (VOC) domain profile.LGUL_ECOLI2-126
 		  2A:2-126
B:2-126
2GLYOXALASE_I_1PS00934 Glyoxalase I signature 1.LGUL_ECOLI5-26
 		  2A:5-26
B:5-26
3GLYOXALASE_I_2PS00935 Glyoxalase I signature 2.LGUL_ECOLI69-81
 		  2A:69-81
B:69-81

(-) Exons   (0, 0)

(no "Exon" information available for 1FA5)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:128
 aligned with LGUL_ECOLI | P0AC81 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
           LGUL_ECOLI     1 MRLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYNWGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYKIELIEEKDAGRGLGN 135
               SCOP domains d1fa5a_ A: Glyoxalase I (lactoylglutathione lyase)                                                                                      SCOP domains
               CATH domains 1fa5A00 A:1-135 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhh...eeeeeeee....eeeeeee........eeeeeee...........eeeeeee..hhhhhhhhhhhh..eeeeeeee......eeeeee.....eeeee..-------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -VOC  PDB: A:2-126 UniProt: 2-126                                                                                             --------- PROSITE (1)
                PROSITE (2) ----GLYOXALASE_I_1        ------------------------------------------GLYOXALASE_I_------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fa5 A   1 MRLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYNWGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYKIELIEE-------GN 135
                                    10        20        30        40        50        60        70        80        90       100       110       120     |   -   | 
                                                                                                                                                       126     134 


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with LGUL_ECOLI | P0AC81 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
           LGUL_ECOLI     1 MRLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYNWGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYKIELIEEKDAGRGLGN 135
               SCOP domains d1fa5b_ B: Glyoxalase I (lactoylglutathione lyase)                                                                                      SCOP domains
               CATH domains 1fa5B00 B:1-135 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhh...eeeeeeee....eeeeeee........eeeeeee...........eeeeeeee.hhhhhhhhhhhh..eeeeeeee......eeeeee.....eeeeee.-------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -VOC  PDB: B:2-126 UniProt: 2-126                                                                                             --------- PROSITE (1)
                PROSITE (2) ----GLYOXALASE_I_1        ------------------------------------------GLYOXALASE_I_------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fa5 B   1 MRLLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYNWGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTTVIAFVEDPDGYKIELIEE-------GN 135
                                    10        20        30        40        50        60        70        80        90       100       110       120     |   -   | 
                                                                                                                                                       126     134
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FA5)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LGUL_ECOLI | P0AC81)
molecular function
    GO:0004462    lactoylglutathione lyase activity    Catalysis of the reaction: (R)-S-lactoylglutathione = glutathione + methylglyoxal.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0019243    methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione    The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LGUL_ECOLI | P0AC81: 1f9z 1fa6 1fa7 1fa8

(-) Related Entries Specified in the PDB File

1f9z NI(II)-BOUND E. COLI GLYOXALASE I
1fa6 CO(II)-BOUND E. COLI GLYOXALASE I
1fa7 CD(II)-BOUND E. COLI GLYOXALASE I
1fa8 APO FORM E. COLI GLYOXALASE I
1fro 1FRO CONTAINS GLYOXALASE I FROM HUMAN