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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF CONSERVED HYPOTHETICAL UPF0122 PROTEIN SAV1236 FROM STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50
 
Authors :  J. R. Walker, X. Xu, C. Virag, M. -L. Mcdonald, S. Houston, K. Buzadzija, M. Vedadi, A. Dharamsi, K. M. Fiebig, A. Savchenko
Date :  20 Oct 04  (Deposition) - 26 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Helix-Turn-Helix, Putative Dna-Binding Protein, Signal Recognition Particle, Upf0122, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Walker, X. Xu, C. Virag, M. -L. Mcdonald, S. Houston, K. Buzadzija, M. Vedadi, A. Dharamsi, K. M. Fiebig, A. Savchenko
1. 7 Angstrom Crystal Structure Of Conserved Hypothetical Upf0122 Protein Sav1236 From Staphylococcus Aureus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL UPF0122 PROTEIN SAV1236
    Atcc: 700699
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPW2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SAV1236
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 46170
    Strain: SUBSP. AUREUS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1XSV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XSV)

(-) Exons   (0, 0)

(no "Exon" information available for 1XSV)

(-) Sequences/Alignments

Asymmetric/Biological Unit
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   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:106
 aligned with Y1236_STAAM | P67248 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:106
                                    14        24        34        44        54        64        74        84        94       104      
          Y1236_STAAM     5 DLVKTLRMNYLFDFYQSLLTNKQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLELYQKFEQRREIYDEMKQHLSNPEQIQRYIQQLEDLE 110
               SCOP domains d1xsva_ A: Hypothetical protein SAV1236                                                                    SCOP domains
               CATH domains 1xsvA00 A:5-110 'winged helix' repressor DNA binding domain                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1xsv A   5 DLVKTLRmNYLFDFYQSLLTNKQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLELYQKFEQRREIYDEmKQHLSNPEQIQRYIQQLEDLE 110
                                   |14        24        34        44        54        64        74        84    |   94       104      
                                  12-MSE                                                                       89-MSE                 


Chain B from PDB  Type:PROTEIN  Length:106
 aligned with Y1236_STAAM | P67248 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:106
                                    14        24        34        44        54        64        74        84        94       104      
          Y1236_STAAM     5 DLVKTLRMNYLFDFYQSLLTNKQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLELYQKFEQRREIYDEMKQHLSNPEQIQRYIQQLEDLE 110
               SCOP domains d1xsvb_ B: Hypothetical protein SAV1236                                                                    SCOP domains
               CATH domains 1xsvB00 B:5-110 'winged helix' repressor DNA binding domain                                                CATH domains
           Pfam domains (1) -UPF0122-1xsvB01 B:6-106                                                                              ---- Pfam domains (1)
           Pfam domains (2) -UPF0122-1xsvB02 B:6-106                                                                              ---- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1xsv B   5 DLVKTLRmNYLFDFYQSLLTNKQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLELYQKFEQRREIYDEmKQHLSNPEQIQRYIQQLEDLE 110
                                   |14        24        34        44        54        64        74        84    |   94       104      
                                  12-MSE                                                                       89-MSE
   Legend:   → Mismatch (orange background)
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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: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Y1236_STAAM | P67248)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016987    sigma factor activity    A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes.
    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:0006352    DNA-templated transcription, initiation    Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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  1xsv
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