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(-) Description

Title :  CRYSTAL STRUCTURE OF YHBO FROM ESCHERICHIA COLI
 
Authors :  J. B. Claude, C. Abergel, J. M. Claverie
Date :  06 Jun 03  (Deposition) - 03 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pfpi/Thij Family, Hypothetical Protein, Complete Proteome, Yhbo, Pfpi, Thij, Bacterial Targets At Igs-Cnrs, France, Bigs, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Claude, C. Abergel, J. M. Claverie
Crystal Structure Of Yhbo From Escherichia Coli
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YHBO
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST17
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: 21 MORE RESIDUES IN NTER (GATEWAY SYSTEM)
    Other Details - Source: N-TERMINAL POLY-HISTIDINE TAG (21 RESIDUES)
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1OI4)

(-) Sites  (0, 0)

(no "Site" information available for 1OI4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OI4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OI4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OI4)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_C56_PFPIPS51276 PfpI endopeptidase domain profile.YHBO_ECOLI3-171
 		  2A:24-192
B:224-392

(-) Exons   (0, 0)

(no "Exon" information available for 1OI4)

(-) 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:192
 aligned with YHBO_ECOLI | P45470 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:192
                                                1                                                                                                                                                                           
                                     -         -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           YHBO_ECOLI     - --------------------MSKKIAVLITDEFEDSEFTSPADEFRKAGHEVITIEKQAGKTVKGKKGEASVTIDKSIDEVTPAEFDALLLPGGHSPDYLRGDNRFVTFTRDFVNSGKPVFAICHGPQLLISADVIRGRKLTAVKPIIIDVKNAGAEFYDQEVVVDKDQLVTSRTPDDLPAFNREALRLLGA 172
               SCOP domains ---------------------d1oi4a1 A:23-192 Hypothetical protein YhbO                                                                                                                                - SCOP domains
               CATH domains 1oi4A00 A:2-193  [code=3.40.50.880, no name defined]                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................eeeee......hhhhhhhhhhhhhh..eeeeee.....eee......eee..ee.hhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee..hhhhhhhhh.....ee..hhhhhhhhhhh..ee.....eee...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------PEPTIDASE_C56_PFPI  PDB: A:24-192 UniProt: 3-171                                                                                                                         - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1oi4 A   2 SYYHHHHHHLESTSLYKKAGLSKKIAVLITDEFEDSEFTSPADEFRKAGHEVITIEKQAGKTVKGKKGEASVTIDKSIDEVTPAEFDALLLPGGHSPDYLRGDNRFVTFTRDFVNSGKPVFAICHGPQLLISADVIRGRKLTAVKPIIIDVKNAGAEFYDQEVVVDKDQLVTSRTPDDLPAFNREALRLLGA 193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with YHBO_ECOLI | P45470 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:174
                              1                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168    
           YHBO_ECOLI     - --MSKKIAVLITDEFEDSEFTSPADEFRKAGHEVITIEKQAGKTVKGKKGEASVTIDKSIDEVTPAEFDALLLPGGHSPDYLRGDNRFVTFTRDFVNSGKPVFAICHGPQLLISADVIRGRKLTAVKPIIIDVKNAGAEFYDQEVVVDKDQLVTSRTPDDLPAFNREALRLLGA 172
               SCOP domains ---d1oi4b1 B:223-392 Hypothetical protein YhbO                                                                                                                               - SCOP domains
               CATH domains 1oi4B00 B:220-393  [code=3.40.50.880, no name defined]                                                                                                                         CATH domains
           Pfam domains (1) --------------------------------DJ-1_PfpI-1oi4B01 B:252-392                                                                                                                  - Pfam domains (1)
           Pfam domains (2) --------------------------------DJ-1_PfpI-1oi4B02 B:252-392                                                                                                                  - Pfam domains (2)
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhh..eeeeee.....eee......eee..ee.hhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee...hhhhhhhh.....ee..hhhhhhhhhhh..ee.....eee...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PEPTIDASE_C56_PFPI  PDB: B:224-392 UniProt: 3-171                                                                                                                        - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1oi4 B 220 AGLSKKIAVLITDEFEDSEFTSPADEFRKAGHEVITIEKQAGKTVKGKKGEASVTIDKSIDEVTPAEFDALLLPGGHSPDYLRGDNRFVTFTRDFVNSGKPVFAICHGPQLLISADVIRGRKLTAVKPIIIDVKNAGAEFYDQEVVVDKDQLVTSRTPDDLPAFNREALRLLGA 393
                                   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389
   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, 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  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YHBO_ECOLI | P45470)
molecular function
    GO:0019172    glyoxalase III activity    Catalysis of the reaction: methylglyoxal + H2O = D-lactate.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
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:0009411    response to UV    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0009268    response to pH    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. pH is a measure of the acidity or basicity of an aqueous solution.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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