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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE DNA BINDING PROTEIN SP_1288 FROM STREPTOCOCCUS PYGENES
 
Authors :  V. Oganesyan, R. Pufan, A. Degiovanni, H. Yokota, R. Kim, S. -H. Kim, Ber Structural Genomics Center (Bsgc)
Date :  29 Jan 04  (Deposition) - 29 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A  (2x)
Keywords :  Putative Dna Binding Protein; Structural Genomics, Signal Recognition Particle, Rna Polymerase Sigma Factor, X-Rat Crystallography, Upf0122, Structure Funded By Nih, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Oganesyan, R. Pufan, A. Degiovanni, H. Yokota, R. Kim, S. H. Kim
Structure Of The Putative Dna-Binding Protein Sp_1288 From Streptococcus Pyogenes.
Acta Crystallogr. , Sect. D V. 60 1266 2004
PubMed-ID: 15213388  |  Reference-DOI: 10.1107/S0907444904009394

(-) Compounds

Molecule 1 - HYPOTHETICAL UPF0122 PROTEIN SPY1201/SPYM3_0842/SPS1042/SPYM18_1152
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PB3.1325B
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GI 15675166
    Gene: SPY1201, SPYM3_0842, SPS1042, SPYM18_1152
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M3
    Organism Taxid: 301448
    Strain: SEROTYPE M3

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (1x):  BC
Biological Unit 3 (2x): A  

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1S7O)

(-) Sites  (0, 0)

(no "Site" information available for 1S7O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S7O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S7O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S7O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S7O)

(-) Exons   (0, 0)

(no "Exon" information available for 1S7O)

(-) Sequences/Alignments

Asymmetric 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:106
 aligned with Y1201_STRP1 | P67253 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:106
                                    16        26        36        46        56        66        76        86        96       106      
          Y1201_STRP1     7 EKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSIDNR 112
               SCOP domains d1s7oa_ A: Hypothetical protein SPy1201                                                                    SCOP domains
               CATH domains 1s7oA00 A:7-112 'winged helix' repressor DNA binding domain                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1s7o A   7 EKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSIDNR 112
                                    16        26        36        46        56        66        76        86        96       106      


Chain A from PDB  Type:PROTEIN  Length:106
 aligned with Y842_STRP3 | P0DG80 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:106
                                    16        26        36        46        56        66        76        86        96       106      
           Y842_STRP3     7 EKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSIDNR 112
               SCOP domains d1s7oa_ A: Hypothetical protein SPy1201                                                                    SCOP domains
               CATH domains 1s7oA00 A:7-112 'winged helix' repressor DNA binding domain                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1s7o A   7 EKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSIDNR 112
                                    16        26        36        46        56        66        76        86        96       106      


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with Y1201_STRP1 | P67253 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:105
                                    15        25        35        45        55        65        75        85        95       105     
          Y1201_STRP1     6 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSID 110
               SCOP domains d1s7ob_ B: Hypothetical protein SPy1201                                                                   SCOP domains
               CATH domains 1s7oB00 B:6-110 'winged helix' repressor DNA binding domain                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1s7o B   6 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSID 110
                                    15        25        35        45        55        65        75        85        95       105     


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with Y842_STRP3 | P0DG80 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:105
                                    15        25        35        45        55        65        75        85        95       105     
           Y842_STRP3     6 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSID 110
               SCOP domains d1s7ob_ B: Hypothetical protein SPy1201                                                                   SCOP domains
               CATH domains 1s7oB00 B:6-110 'winged helix' repressor DNA binding domain                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1s7o B   6 IEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSID 110
                                    15        25        35        45        55        65        75        85        95       105     


Chain C from PDB  Type:PROTEIN  Length:108
 aligned with Y1201_STRP1 | P67253 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:108
                                    14        24        34        44        54        64        74        84        94       104        
          Y1201_STRP1     5 EIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSIDNR 112
               SCOP domains d1s7oc_ C: Hypothetical protein SPy1201                                                                      SCOP domains
               CATH domains 1s7oC00 C:5-112 'winged helix' repressor DNA binding domain                                                  CATH domains
           Pfam domains (1) -UPF0122-1s7oC01 C:6-106                                                                              ------ Pfam domains (1)
           Pfam domains (2) -UPF0122-1s7oC02 C:6-106                                                                              ------ Pfam domains (2)
           Pfam domains (3) -UPF0122-1s7oC03 C:6-106                                                                              ------ Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1s7o C   5 EIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSIDNR 112
                                    14        24        34        44        54        64        74        84        94       104        


Chain C from PDB  Type:PROTEIN  Length:108
 aligned with Y842_STRP3 | P0DG80 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:108
                                    14        24        34        44        54        64        74        84        94       104        
           Y842_STRP3     5 EIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSIDNR 112
               SCOP domains d1s7oc_ C: Hypothetical protein SPy1201                                                                      SCOP domains
               CATH domains 1s7oC00 C:5-112 'winged helix' repressor DNA binding domain                                                  CATH domains
           Pfam domains (1) -UPF0122-1s7oC01 C:6-106                                                                              ------ Pfam domains (1)
           Pfam domains (2) -UPF0122-1s7oC02 C:6-106                                                                              ------ Pfam domains (2)
           Pfam domains (3) -UPF0122-1s7oC03 C:6-106                                                                              ------ Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1s7o C   5 EIEKTNRMNALFEFYAALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMYSDYVVRSEIFDDMIAHYPHDEYLQEKISILTSIDNR 112
                                    14        24        34        44        54        64        74        84        94       104
   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, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (5, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Y842_STRP3 | P0DG80)
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.

Chain A,B,C   (Y1201_STRP1 | P67253)
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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  Y842_STRP3 | P0DG80
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 Related Entries

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

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