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(-) Description

Title :  CRYSTAL STRUCTURE OF DMPI FROM HELICOBACTER PYLORI DETERMINED TO 1.9 ANGSTROMS RESOLUTION
 
Authors :  M. L. Hackert, C. P. Whitman, J. J. Almrud, R. Dasgupta, A. D. Kern, R. M. C
Date :  06 Mar 10  (Deposition) - 01 Sep 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  4-Oxalocrotonate Tautomerase, Catalytic Proline, Hexamer, Beta-Alpha- Beta, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Almrud, R. Dasgupta, R. M. Czerwinski, A. D. Kern, M. L. Hackert, C. P. Whitman
Kinetic And Structural Characterization Of Dmpi From Helicobacter Pylori And Archaeoglobus Fulgidus, Two 4-Oxalocrotonate Tautomerase Family Members.
Bioorg. Chem. V. 38 252 2010
PubMed-ID: 20709352  |  Reference-DOI: 10.1016/J.BIOORG.2010.07.002

(-) Compounds

Molecule 1 - PROBABLE TAUTOMERASE HP_0924
    Chains: A, B, C, D, E, F
    EC Number: 5.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector: PET24A(+)
    Expression System Vector Type: PLASMID
    Gene: 899453, HP_0924
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3M21)

(-) Sites  (0, 0)

(no "Site" information available for 3M21)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M21)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:13 -Pro A:14
2Gly B:13 -Pro B:14
3Gly C:13 -Pro C:14
4Gly D:13 -Pro D:14
5Gly E:13 -Pro E:14
6Gly F:13 -Pro F:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M21)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M21)

(-) Exons   (0, 0)

(no "Exon" information available for 3M21)

(-) 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:65
 aligned with Y924_HELPY | O25581 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:65
                                    11        21        31        41        51        61     
            Y924_HELPY    2 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQ 66
               SCOP domains d3m21a_ A: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee.....eee..eehhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  3m21 A  1 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQ 65
                                    10        20        30        40        50        60     


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with Y924_HELPY | O25581 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:66
                                    11        21        31        41        51        61      
            Y924_HELPY    2 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQK 67
               SCOP domains d3m21b_ B: automated matches                                       SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee.....eee..eehhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3m21 B  1 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQK 66
                                    10        20        30        40        50        60      


Chain C from PDB  Type:PROTEIN  Length:63
 aligned with Y924_HELPY | O25581 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:63
                                    11        21        31        41        51        61   
            Y924_HELPY    2 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHL 64
               SCOP domains d3m21c_ C: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhhhhhhh..hhhh.eeeeee.....eee..ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  3m21 C  1 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHL 63
                                    10        20        30        40        50        60   


Chain D from PDB  Type:PROTEIN  Length:66
 aligned with Y924_HELPY | O25581 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:66
                                    11        21        31        41        51        61      
            Y924_HELPY    2 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQK 67
               SCOP domains d3m21d_ D: automated matches                                       SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee.....eee..eehhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3m21 D  1 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQK 66
                                    10        20        30        40        50        60      


Chain E from PDB  Type:PROTEIN  Length:65
 aligned with Y924_HELPY | O25581 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:65
                                    11        21        31        41        51        61     
            Y924_HELPY    2 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQ 66
               SCOP domains d3m21e_ E: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee.....eee..ee.hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  3m21 E  1 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQ 65
                                    10        20        30        40        50        60     


Chain F from PDB  Type:PROTEIN  Length:67
 aligned with Y924_HELPY | O25581 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:67
                                    11        21        31        41        51        61       
            Y924_HELPY    2 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQKN 68
               SCOP domains d3m21f_ F: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
           Pfam domains (1) Tautomerase-3m21F01 F:1-63                                     ---- Pfam domains (1)
           Pfam domains (2) Tautomerase-3m21F02 F:1-63                                     ---- Pfam domains (2)
           Pfam domains (3) Tautomerase-3m21F03 F:1-63                                     ---- Pfam domains (3)
           Pfam domains (4) Tautomerase-3m21F04 F:1-63                                     ---- Pfam domains (4)
           Pfam domains (5) Tautomerase-3m21F05 F:1-63                                     ---- Pfam domains (5)
           Pfam domains (6) Tautomerase-3m21F06 F:1-63                                     ---- Pfam domains (6)
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhhhhhhhh.hhhh.eeeeee.....eee..eehhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  3m21 F  1 PFINIKLVPENGGPTNEQKQQLIEGVSDLMVKVLNKNKASIVVIIDEVDSNNYGLGGESVHHLRQKN 67
                                    10        20        30        40        50        60
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M21)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: MIF (36)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Y924_HELPY | O25581)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.

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  Sites
(no "Sites" information available for 3m21)
 
  Cis Peptide Bonds
    Gly A:13 - Pro A:14   [ RasMol ]  
    Gly B:13 - Pro B:14   [ RasMol ]  
    Gly C:13 - Pro C:14   [ RasMol ]  
    Gly D:13 - Pro D:14   [ RasMol ]  
    Gly E:13 - Pro E:14   [ RasMol ]  
    Gly F:13 - Pro F:14   [ RasMol ]  
 

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  3m21
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  Y924_HELPY | O25581
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 Related Entries

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

UniProtKB/Swiss-Prot
        Y924_HELPY | O25581: 2orm

(-) Related Entries Specified in the PDB File

2orm 3m20