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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MARR FAMILY TRANSCRIPTIONAL REGULATOR SPO1453 FROM SILICIBACTER POMEROYI DSS-3
 
Authors :  Y. Kim, L. Volkart, L. Keigher, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  26 Feb 08  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Marr, Helix-Turn-Hleix, Transcriptional Regulator, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, L. Volkart, L. Keigher, A. Joachimiak
Crystal Structure Of The Marr Family Transcriptional Regulator Spo1453 From Silicibacter Pomeroyi.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, MARR FAMILY
    Atcc: 700808
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SPO1453
    Organism Scientific: SILICIBACTER POMEROYI DSS-3
    Organism Taxid: 246200
    Strain: DSS-3 / DSM 15171

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 19)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3SO46Ligand/IonSULFATE ION
Biological Unit 2 (3, 38)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MSE20Mod. Amino AcidSELENOMETHIONINE
3SO412Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:39 , ARG B:73BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWAREARG A:73 , GLN A:77 , GLN B:77BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREARG A:86 , ALA A:88 , ARG A:99BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREARG A:99 , THR A:101 , ASP A:102BINDING SITE FOR RESIDUE SO4 A 204
5AC5SOFTWAREALA B:54 , ARG B:59 , ARG B:97BINDING SITE FOR RESIDUE SO4 B 205
6AC6SOFTWAREARG A:59 , ARG A:97BINDING SITE FOR RESIDUE SO4 A 206
7AC7SOFTWAREARG A:44 , LEU A:63 , TYR B:16BINDING SITE FOR RESIDUE GOL A 207
8AC8SOFTWARETYR A:16 , ARG B:44 , LEU B:63BINDING SITE FOR RESIDUE GOL B 208
9AC9SOFTWAREARG B:86 , ALA B:88 , ARG B:99BINDING SITE FOR RESIDUE GOL B 209

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CDH)

(-) Exons   (0, 0)

(no "Exon" information available for 3CDH)

(-) 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:134
 aligned with Q5LTG1_RUEPO | Q5LTG1 from UniProtKB/TrEMBL  Length:152

    Alignment length:140
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146
         Q5LTG1_RUEPO     7 DTFVSGYLLYLLAASSEEASAQFHDHIRAQGLRVPEWRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAESLVASARAHETRLLSALADTDAARIKGVLRTLLDVLD 146
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cdhA00 A:7-146 'winged helix' repressor DNA binding domain                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhh..eee..------...eeehhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cdh A   7 DTFVSGYLLYLLAASSEEASAQFHDHIRAQGLRVPEWRVLACLVDNDAmmITRLAKLSLmEQSRmTRIVDQmDARGLVTRVA------RVRVRLTDDGRALAESLVASARAHETRLLSALADTDAARIKGVLRTLLDVLD 146
                                    16        26        36        46        56        66    |   76 |      86 |      96       106       116       126       136       146
                                                                           55-MSE     66-MSE|     78-MSE    88     95                                                   
                                                                            56-MSE         71-MSE                                                                       


Chain B from PDB  Type:PROTEIN  Length:136
 aligned with Q5LTG1_RUEPO | Q5LTG1 from UniProtKB/TrEMBL  Length:152

    Alignment length:140
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146
         Q5LTG1_RUEPO     7 DTFVSGYLLYLLAASSEEASAQFHDHIRAQGLRVPEWRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAESLVASARAHETRLLSALADTDAARIKGVLRTLLDVLD 146
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cdhB00 B:7-146 'winged helix' repressor DNA binding domain                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....eehhhhhhhhh.hhhhhhhhhhhhhhh..eee....----..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cdh B   7 DTFVSGYLLYLLAASSEEASAQFHDHIRAQGLRVPEWRVLACLVDNDAmmITRLAKLSLmEQSRmTRIVDQmDARGLVTRVADA----RVRVRLTDDGRALAESLVASARAHETRLLSALADTDAARIKGVLRTLLDVLD 146
                                    16        26        36        46        56        66    |   76 |      86   |    96       106       116       126       136       146
                                                                           55-MSE     66-MSE|     78-MSE      90   95                                                   
                                                                            56-MSE         71-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3CDH)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5LTG1_RUEPO | Q5LTG1)
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: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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