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(-) Description

Title :  THE STRUCTURE OF THE STRESS RESPONSE PROTEIN DR1199 FROM DEINOCOCCUS RADIODURANS: A MEMBER OF THE DJ-1 SUPERFAMILY
 
Authors :  E. Fioravanti, M. A. Dura, D. Lascoux, E. Micossi, S. Mcsweeney
Date :  09 Apr 08  (Deposition) - 28 Oct 08  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cysteine Sulfenic Acid, Dj-1/Thij/Pfpi Superfamily, Protease, Hydrolase, Stress Response (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Fioravanti, M. A. Dura, D. Lascoux, E. Micossi, B. Franzetti, S. Mcsweeney
Structure Of The Stress Response Protein Dr1199 From Deinococcus Radiodurans: A Member Of The Dj-1 Superfamily.
Biochemistry V. 47 11581 2008
PubMed-ID: 18850720  |  Reference-DOI: 10.1021/BI800882V

(-) Compounds

Molecule 1 - PROTEASE I
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: DE3
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Other Details: CYSTEINE 115 MODIFIED TO CYSTEINE SULFENIC ACID (CSO)
    Strain: R1
    Synonym: DR1199

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:179 , GLU A:182 , HIS A:185 , HOH A:2073 , HOH A:2085BINDING SITE FOR RESIDUE MG A1191

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VRN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VRN)

(-) 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:185
 aligned with Q9RV31_DEIRA | Q9RV31 from UniProtKB/TrEMBL  Length:190

    Alignment length:185
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185     
         Q9RV31_DEIRA     6 DLTGKKIAILAADGVEEIELTSPRAAIEAAGGTTELISLEPGEIQSMKGDIEPQEKYRVDHVVSEVQVSDYDGLLLPGGTVNPDKLRLEEGAMKFVRDMYDAGKPIAAICHGPWSLSETGIAQGLKMTSWPSLKRELTLAGAQWVDEECVTDKGVVTSRKPDDLPAFNKKIVEEFAEGDHSSRRK 190
               SCOP domains d2vrna_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains 2vrnA00 A:6-190  [code=3.40.50.880, no name defined]                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhh..eeeeee....eeeeee...eeeeeee..ee.hhhhhhhh.eeee...hhhhhhhh.hhhhhhhhhhhhhh...eee....hhhhhhh......ee..hhhhhhhhhhh..ee.....eee..eee..hhhhhhhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrn A   6 DLTGKKIAILAADGVEEIELTSPRAAIEAAGGTTELISLEPGEIQSMKGDIEPQEKYRVDHVVSEVQVSDYDGLLLPGGTVNPDKLRLEEGAMKFVRDMYDAGKPIAAIcHGPWSLSETGIAQGLKMTSWSSLKRELTLAGAQWVDEECVTDKGVVTSRKPDDLPAFNKKIVEEFAEGDHSSRRK 190
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185     
                                                                                                                                       115-CSO                                                                       


Chain B from PDB  Type:PROTEIN  Length:185
 aligned with Q9RV31_DEIRA | Q9RV31 from UniProtKB/TrEMBL  Length:190

    Alignment length:185
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185     
         Q9RV31_DEIRA     6 DLTGKKIAILAADGVEEIELTSPRAAIEAAGGTTELISLEPGEIQSMKGDIEPQEKYRVDHVVSEVQVSDYDGLLLPGGTVNPDKLRLEEGAMKFVRDMYDAGKPIAAICHGPWSLSETGIAQGLKMTSWPSLKRELTLAGAQWVDEECVTDKGVVTSRKPDDLPAFNKKIVEEFAEGDHSSRRK 190
               SCOP domains d2vrnb_ B: automated matches                                                                                                                                                              SCOP domains
               CATH domains 2vrnB00 B:6-190  [code=3.40.50.880, no name defined]                                                                                                                                      CATH domains
           Pfam domains (1) --------------------------------DJ-1_PfpI-2vrnB01 B:38-181                                                                                                                      --------- Pfam domains (1)
           Pfam domains (2) --------------------------------DJ-1_PfpI-2vrnB02 B:38-181                                                                                                                      --------- Pfam domains (2)
         Sec.struct. author .....eeeee....eehhhhhhhhhhhhhh..eeeeee....eeeeee...eeeeeee..ee.hhhhhhhh.eeee...hhhhhhhh.hhhhhhhhhhhhhh...eee....hhhhhhh......ee..hhhhhhhhhhh..ee....eeee..eeee.hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrn B   6 DLTGKKIAILAADGVEEIELTSPRAAIEAAGGTTELISLEPGEIQSMKGDIEPQEKYRVDHVVSEVQVSDYDGLLLPGGTVNPDKLRLEEGAMKFVRDMYDAGKPIAAIcHGPWSLSETGIAQGLKMTSWSSLKRELTLAGAQWVDEECVTDKGVVTSRKPDDLPAFNKKIVEEFAEGDHSSRRK 190
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185     
                                                                                                                                       115-CSO
   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) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Glutaminase_I (73)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9RV31_DEIRA | Q9RV31)
molecular function
    GO:0019172    glyoxalase III activity    Catalysis of the reaction: methylglyoxal + H2O = D-lactate.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0019249    lactate biosynthetic process    The chemical reactions and pathways resulting in the formation of lactate, the anion of lactic acid.
    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.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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