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(-) Description

Title :  CRYSTAL STRUCTURE OF MARR FAMILY TRANSCRIPTION REGULATOR SP03579
 
Authors :  Y. Kim, L. Volkart, L. Keigher, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  03 Dec 07  (Deposition) - 18 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Marr Family, Helix-Turn-Helix, Trasnscription Regulator, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, L. Volkart, L. Keigher, A. Joachimiak
Crystal Structure Of Marr Family Transcription Regulator Sp03579.
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: SPO3579
    Organism Scientific: SILICIBACTER POMEROYI DSS-3
    Organism Taxid: 246200
    Strain: DSS-3, DSM 15171

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1EOH7Ligand/IonETHANOL
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:19 , VAL B:12 , GLN B:13 , ARG B:16 , HOH B:350BINDING SITE FOR RESIDUE EOH B 150
2AC2SOFTWAREVAL A:26 , GLU A:112 , HOH A:179 , TYR B:9BINDING SITE FOR RESIDUE EOH A 150
3AC3SOFTWAREGLY A:34 , HOH A:162 , SER B:92 , HOH B:254BINDING SITE FOR RESIDUE EOH A 151
4AC4SOFTWAREHIS A:89 , THR B:36 , GLN B:39BINDING SITE FOR RESIDUE EOH B 151
5AC5SOFTWAREPHE A:142 , GLU B:112 , EOH B:153BINDING SITE FOR RESIDUE EOH B 152
6AC6SOFTWARETYR A:9 , EOH A:152 , VAL B:26 , LEU B:116 , EOH B:152BINDING SITE FOR RESIDUE EOH B 153
7AC7SOFTWARETYR A:9 , EOH B:153 , HOH B:249BINDING SITE FOR RESIDUE EOH A 152

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BJ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BJ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BJ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BJ6)

(-) Exons   (0, 0)

(no "Exon" information available for 3BJ6)

(-) 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:152
 aligned with Q5LMI4_RUEPO | Q5LMI4 from UniProtKB/TrEMBL  Length:149

    Alignment length:152
                               1                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147  
         Q5LMI4_RUEPO     - ---MTHETDQLYQAVQATRPLLRNITAAVERGTLREGVTVGQRAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITAIRADEMAKLALFSEGFSSVELTAYHKVQLALTRFFADLAKEA 149
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bj6A00 A:-2-149 'winged helix' repressor DNA binding domain                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee.........eeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bj6 A  -2 SNAmTHETDQLYQAVQATRPLLRNITAAVERGTLREGVTVGQRAILEGLSLTPGATAPQLGAALQmKRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITAIRADEmAKLALFSEGFSSVELTAYHKVQLALTRFFADLAKEA 149
                               |     7        17        27        37        47        57     |  67        77        87        97       107     | 117       127       137       147  
                               |                                                            63-MSE                                           113-MSE                                
                               1-MSE                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:151
 aligned with Q5LMI4_RUEPO | Q5LMI4 from UniProtKB/TrEMBL  Length:149

    Alignment length:151
                              1                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148 
         Q5LMI4_RUEPO     - --MTHETDQLYQAVQATRPLLRNITAAVERGTLREGVTVGQRAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITAIRADEMAKLALFSEGFSSVELTAYHKVQLALTRFFADLAKEA 149
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bj6B00 B:-1-149 'winged helix' repressor DNA binding domain                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.........eeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bj6 B  -1 NAmTHETDQLYQAVQATRPLLRNITAAVERGTLREGVTVGQRAILEGLSLTPGATAPQLGAALQmKRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITAIRADEmAKLALFSEGFSSVELTAYHKVQLALTRFFADLAKEA 149
                              |      8        18        28        38        48        58    |   68        78        88        98       108    |  118       128       138       148 
                              1-MSE                                                        63-MSE                                           113-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  (0, 0)

(no "SCOP Domain" information available for 3BJ6)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BJ6)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5LMI4_RUEPO | Q5LMI4)
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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