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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PERR-OX HIGHLIGHTS 2-OXO-HISTIDINE FORMATION
 
Authors :  D. A. K. Traore
Date :  05 Oct 07  (Deposition) - 14 Oct 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  2-Oxo-Histidine, Perr-Ox, Cytoplasm, Dna-Binding, Manganese, Oxidation, Repressor, Transcription, Transcription Regulation, Zinc, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Traore, A. El Ghazouani, L. Jacquamet, F. Borel, J. L. Ferrer, D. Lascoux, J. L. Ravanat, M. Jaquinod, G. Blondin, C. Caux-Thang, V. Duarte, J. M. Latour
Structural And Functional Characterization Of 2-Oxo-Histidine In Oxidized Perr Protein.
Nat. Chem. Biol. V. 5 53 2009
PubMed-ID: 19079268  |  Reference-DOI: 10.1038/NCHEMBIO.133
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXIDE OPERON REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1OHI6Mod. Amino Acid3-(2-OXO-2H-IMIDAZOL-4-YL)-L-ALANINE
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:96 , CYS A:99 , CYS A:136 , CYS A:139BINDING SITE FOR RESIDUE ZN A 146
2AC2SOFTWARECYS B:96 , CYS B:99 , CYS B:136 , CYS B:139BINDING SITE FOR RESIDUE ZN B 146

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RGV)

(-) 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:141
 aligned with PERR_BACSU | P71086 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:141
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 
           PERR_BACSU     4 HELKEALETLKETGVRITPQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFVTSDHYHAICENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVCQECSKKEN 144
               SCOP domains d2rgva_ A: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeee.......eeee....eeeeee.....eee.....hhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rgv A   4 HELKEALETLKETGVRITPQRHAILEYLVNSMAhPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFVTSDhYhAICENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVCQECSKKEN 144
                                    13        23        33   |    43        53        63        73        83       |93       103       113       123       133       143 
                                                            37-OHI                                                91-OHI                                                 
                                                                                                                    93-OHI                                               


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with PERR_BACSU | P71086 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142   
           PERR_BACSU     3 AHELKEALETLKETGVRITPQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFVTSDHYHAICENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVCQECSKKENH 145
               SCOP domains d2rgvb_ B: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------FUR-2rgvB01 B:15-133                                                                                                   ------------ Pfam domains (1)
           Pfam domains (2) ------------FUR-2rgvB02 B:15-133                                                                                                   ------------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhhhhhhhh..eeee.......eeee....eeeeee.....eee.....hhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rgv B   3 AHELKEALETLKETGVRITPQRHAILEYLVNSMAhPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFVTSDhYhAICENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVCQECSKKENH 145
                                    12        22        32    |   42        52        62        72        82        92|      102       112       122       132       142   
                                                             37-OHI                                                91-OHI                                                  
                                                                                                                     93-OHI
   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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RGV)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Family: FUR (5)
(-)
Bacillus subtilis (1)
1aFUR-2rgvB01B:15-133
1bFUR-2rgvB02B:15-133

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PERR_BACSU | P71086)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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.

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  2rgv
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 Related Entries

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

UniProtKB/Swiss-Prot
        PERR_BACSU | P71086: 2fe3 3f8n

(-) Related Entries Specified in the PDB File

2fe3 APO-PERR-ZN (ID 2FE3) IS THE FULLY REDUCED FORM OF BS-PERR