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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI YEBC
 
Authors :  J. Jia, C. Smith, V. V. Lunin, A. Matte, M. Cygler, Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)
Date :  21 Dec 01  (Deposition) - 17 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta, Two-Domains, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  
Unpublished
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN YEBC
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YEBC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: YEBC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1KON)

(-) 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:233
 aligned with YEBC_ECOLI | P0A8A0 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:244
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    
           YEBC_ECOLI     3 GHSKWANTRHRKAAQDAKRGKIFTKIIRELVTAAKLGGGDPDANPRLRAAVDKALSNNMTRDTLNRAIARGVGGDDDANMETIIYEGYGPGGTAIMIECLSDNRNRTVAEVRHAFSKCGGNLGTDGSVAYLFSKKGVISFEKGDEDTIMEAALEAGAEDVVTYDDGAIDVYTAWEEMGKVRDALEAAGLKADSAEVSMIPSTKADMDAETAPKLMRLIDMLEDCDDVQEVYHNGEISDEVAATL 246
               SCOP domains d1kona_ A: Hypothetical protein YebC                                                                                                                                                                                                                 SCOP domains
               CATH domains 1konA01 A:3-81  [code=1.10.10.200, n     o name defined]                       1konA02 A:82-129,A:205-246                      1konA03 A:130-204  [code=3.30.70.980, no name defined]                     1konA02 A:82-129,A:205-246                 CATH domains
               Pfam domains --Transcrip_reg-1konA01 A:5-237                                                                                                                                                                                                            --------- Pfam domains
         Sec.struct. author ...hhhhh.........hhhhhhhhhhhhhhhhhhh-----.....hhhhhhhhhhh..hhhhhhhhhh..------...eeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhhh...ee.....hhh.eeeeeeeee...hhhhhhhhhhhhh..eeee.....eeeeee..hhhhhhhhhhhh.....eeeeeeee..........hhhhhhhhhhhhhh..eeeeee....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kon A   3 GHSKWANTRHRKAAQDAKRGKIFTKIIRELVTAAKL-----DANPRLRAAVDKALSNNMTRDTLNRAIARG------ANMETIIYEGYGPGGTAIMIECLSDNRNRTVAEVRHAFSKCGGNLGTDGSVAYLFSKKGVISFEKGDEDTIMEAALEAGAEDVVTYDDGAIDVYTAWEEMGKVRDALEAAGLKADSAEVSMIPSTKADMDAETAPKLMRLIDMLEDCDDVQEVYHNGEISDEVAATL 246
                                    12        22        32     |   - |      52        62        72|      |82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    
                                                              38    44                           73     80
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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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Transcrip_reg] (3)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YEBC_ECOLI | P0A8A0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0010212    response to ionizing radiation    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 ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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