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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSCRIPTION REGULATORY PROTEIN SLYA FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH SALICYLATE LIGANDS
 
Authors :  I. Le Trong, P. S. Brzovic, F. C. Fang, S. J. Libby, R. E. Stenkamp
Date :  10 Jun 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Slya, Marr, Salmonella, Wing-Helix, Transcription Regulator, Activator, Dna-Binding, Repressor, Transcription Regulation, Virulence (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. S. Brzovic, I. Le Trong, W. W. Navarre, F. C. Fang, R. E. Stenkamp, S. J. Libby
Crystal Structure Of Transcription Regulatory Protein Slya From Salmonella Typhimurium In Complex With Salicylate Ligands.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR SLYA
    Atcc14028S
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET16B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSLYA, STM1444
    Organism ScientificSALMONELLA TYPHIMURIUM
    Organism Taxid602
    StrainSGSG 2262
    SynonymSALMOLYSIN, CYTOLYSIN SLYA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)A 
Biological Unit 2 (2x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SAL6Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SAL6Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1SAL6Ligand/Ion2-HYDROXYBENZOIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:8 , ALA A:11 , ARG A:15 , TRP A:17 , ARG A:18 , HIS A:39BINDING SITE FOR RESIDUE SAL A 301
2AC2SOFTWARESER B:8 , ALA B:11 , ARG B:15 , ARG B:18 , ILE B:21 , HIS B:39BINDING SITE FOR RESIDUE SAL B 302
3AC3SOFTWAREARG A:24 , LYS A:110 , GLU A:114BINDING SITE FOR RESIDUE SAL A 303
4AC4SOFTWAREARG B:24 , LYS B:110 , GLU B:114BINDING SITE FOR RESIDUE SAL B 304
5AC5SOFTWARETHR A:33 , THR A:37 , ILE A:59 , THR A:67BINDING SITE FOR RESIDUE SAL A 305
6AC6SOFTWARETHR B:33 , THR B:37 , ILE B:59 , THR B:67BINDING SITE FOR RESIDUE SAL B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DEU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DEU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DEU)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_MARR_2PS50995 MarR-type HTH domain profile.SLYA_SALTY2-135
 
  2A:3-136
B:3-136
2HTH_MARR_1PS01117 MarR-type HTH domain signature.SLYA_SALTY62-96
 
  2A:63-97
B:63-97
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_MARR_2PS50995 MarR-type HTH domain profile.SLYA_SALTY2-135
 
  2A:3-136
-
2HTH_MARR_1PS01117 MarR-type HTH domain signature.SLYA_SALTY62-96
 
  2A:63-97
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_MARR_2PS50995 MarR-type HTH domain profile.SLYA_SALTY2-135
 
  2-
B:3-136
2HTH_MARR_1PS01117 MarR-type HTH domain signature.SLYA_SALTY62-96
 
  2-
B:63-97

(-) Exons   (0, 0)

(no "Exon" information available for 3DEU)

(-) 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:132
 aligned with SLYA_SALTY | P40676 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
           SLYA_SALTY     1 MESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKADALIAEMEEVIHKTRGEILAGISSEEIELLIKLIAKLEHNIMEL 140
               SCOP domains d3deua1 A:2-141 Transcriptional regulator SlyA                                                                                               SCOP domains
               CATH domains 3deuA00 A:2-141 'winged helix' repressor DNA binding domain                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eehhhhhhhhh.hhhhhhhhhhhhhhh..eee.--------.eeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_MARR_2  PDB: A:3-136 UniProt: 2-135                                                                                               ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------HTH_MARR_1  PDB: A:63-97           -------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3deu A   2 LESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQ--------KRIKLTEKAEPLIAEMEEVIHKTRGEILAGISSEEIELLIKLIAKLEHNIMEL 141
                                    11        21        31        41        51        61        71        |-       |91       101       111       121       131       141
                                                                                                         80       89                                                    

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with SLYA_SALTY | P40676 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
           SLYA_SALTY     1 MESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKADALIAEMEEVIHKTRGEILAGISSEEIELLIKLIAKLEHNIMEL 140
               SCOP domains d3deub_ B: Transcriptional regulator SlyA                                                                                                    SCOP domains
               CATH domains 3deuB00 B:2-141 'winged helix' repressor DNA binding domain                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhh..ee.----------..ee..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_MARR_2  PDB: B:3-136 UniProt: 2-135                                                                                               ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------HTH_MARR_1  PDB: B:63-97           -------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3deu B   2 LESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISR----------RIKLTEKAEPLIAEMEEVIHKTRGEILAGISSEEIELLIKLIAKLEHNIMEL 141
                                    11        21        31        41        51        61        71       | -        91       101       111       121       131       141
                                                                                                        79         90                                                   

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DEU)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SLYA_SALTY | P40676)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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.

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        SLYA_SALTY | P406763q5f 3qpt

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