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(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA THYPHIMURIUM LT2 GLYOXALASE II
 
Authors :  N. R. Leite, V. A. Campos Bermudez, R. Krogh, G. Oliva, F. C. Soncini, A.
Date :  25 Jun 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Glyoxalase Ii (Hydroxyacylglutathione Hydrolase), Metallo-B-Lactamase Superfamily, Salmonella Typhimurium Lt2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Campos-Bermudez, N. R. Leite, R. Krog, A. J. Costa-Filho, F. C. Soncini, G. Oliva, A. J. Vila
Biochemical And Structural Characterization Of Salmonella Typhimurium Glyoxalase Ii: New Insights Into Metal Ion Selectivity
Biochemistry V. 46 11069 2007
PubMed-ID: 17764159  |  Reference-DOI: 10.1021/BI7007245

(-) Compounds

Molecule 1 - HYDROXYACYLGLUTATHIONE HYDROLASE
    Chains: A
    EC Number: 3.1.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GLOB
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2FE2Ligand/IonFE (III) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:57 , HIS A:58 , ASP A:127 , HIS A:165 , FE A:253 , HOH A:606 , HOH A:692BINDING SITE FOR RESIDUE FE A 252
2AC2SOFTWAREHIS A:53 , HIS A:55 , HIS A:110 , ASP A:127 , FE A:252 , HOH A:607 , HOH A:692BINDING SITE FOR RESIDUE FE A 253
3AC3SOFTWAREPRO A:156 , ASP A:157BINDING SITE FOR RESIDUE EDO A 254
4AC4SOFTWAREGLN A:147BINDING SITE FOR RESIDUE EDO A 255
5AC5SOFTWARETYR A:146 , LEU A:149 , MET A:150 , ASN A:153 , PHE A:216 , LEU A:217 , THR A:219 , HOH A:454BINDING SITE FOR RESIDUE EDO A 256
6AC6SOFTWAREASN A:4 , SER A:5 , ALA A:38 , GLU A:41 , HIS A:42BINDING SITE FOR RESIDUE EDO A 257
7AC7SOFTWAREARG A:23 , PRO A:46 , GLN A:71 , HOH A:582 , HOH A:722BINDING SITE FOR RESIDUE EDO A 258
8AC8SOFTWARELEU A:3 , ASN A:4 , SER A:5 , MET A:201 , HOH A:294 , HOH A:296BINDING SITE FOR RESIDUE EDO A 259

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QED)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:120 -Pro A:121
2Leu A:203 -Pro A:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QED)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QED)

(-) Exons   (0, 0)

(no "Exon" information available for 2QED)

(-) 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:252
 aligned with GLO2_SALTY | Q8ZRM2 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:252
                             1                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249  
           GLO2_SALTY     - -MNLNSIPAFQDNYIWVLTNDEGRCVIVDPGEAAPVLKAIAEHKWMPEAIFLTHHHHDHVGGVKELLQHFPQMTVYGPAETQDKGATHLVGDGDTIRVLGEKFTLFATPGHTLGHVCYFSRPYLFCGDTLFSGGCGRLFEGTPSQMYQSLMKINSLPDDTLICCAHEYTLANIKFALSILPHDSFINEYYRKVKELRVKKQMTLPVILKNERKINLFLRTEDIDLINEINKETILQQPEARFAWLRSKKDTF 251
               SCOP domains -d2qeda1 A:1-251 Glyoxalase II (hydroxyacylglutathione hydrolase)                                                                                                                                                                                            SCOP domains
               CATH domains 2qedA00 A:0-251 Metallo-beta-lactamase, chain A                                                                                                                                                                                                              CATH domains
               Pfam domains -------Lactamase_B-2qedA01 A:7-165                                                                                                                                    -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeee....eeeee...hhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh...eeeehhhhhhhh..ee.....eeee..eeeeeee........eeeee..eeeee..ee..ee......hhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qed A   0 SMNLNSIPAFQDNYIWVLTNDEGRCVIVDPGEAAPVLKAIAEHKWMPEAIFLTHHHHDHVGGVKELLQHFPQMTVYGPAETQDKGATHLVGDGDTIRVLGEKFTLFATPGHTLGHVCYFSRPYLFCGDTLFSGGCGRLFEGTPSQMYQSLMKINSLPDDTLICCAHEYTLANIKFALSILPHDSFINEYYRKVKELRVKKQMTLPVILKNERKINLFLRTEDIDLINEINKETILQQPEARFAWLRSKKDTF 251
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLO2_SALTY | Q8ZRM2)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004416    hydroxyacylglutathione hydrolase activity    Catalysis of the reaction: (S)-(2-hydroxyacyl)glutathione + H2O = glutathione + a 2-hydroxy carboxylate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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