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(-) Description

Title :  CRYSTAL STRUCTURE OF A LACI FAMILY TRANSCRIPTIONAL REGULATOR FROM SILICIBACTER POMEROYI
 
Authors :  J. B. Bonanno, J. Freeman, K. T. Bain, M. Iizuka, S. Ozyurt, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  07 Aug 08  (Deposition) - 26 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Transcription, Dna-Binding, Plasmid, Transcription Regulation, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, J. Freeman, K. T. Bain, M. Iizuka, S. Ozyurt, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A Laci Family Transcriptional Regulator From Silicibacter Pomeroyi
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, LACI FAMILY
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPOA0242
    Organism Scientific: SILICIBACTER POMEROYI
    Organism Taxid: 89184

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3E3M)

(-) Sites  (0, 0)

(no "Site" information available for 3E3M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E3M)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Pro A:228 -Pro A:229
2Val A:274 -Pro A:275
3Ser A:293 -Pro A:294
4Pro B:228 -Pro B:229
5Val B:274 -Pro B:275
6Ser B:293 -Pro B:294
7Pro C:228 -Pro C:229
8Val C:274 -Pro C:275
9Ser C:293 -Pro C:294
10Pro D:228 -Pro D:229
11Val D:274 -Pro D:275
12Ser D:293 -Pro D:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E3M)

(-) Exons   (0, 0)

(no "Exon" information available for 3E3M)

(-) 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:270
 aligned with Q5LKY7_RUEPO | Q5LKY7 from UniProtKB/TrEMBL  Length:346

    Alignment length:278
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338        
         Q5LKY7_RUEPO    69 GFVGLLLPSLNNLHFAQTAQSLTDVLEQGGLQLLLGYTAYSPEREEQLVETMLRRRPEAMVLSYDGHTEQTIRLLQRASIPIVEIWEKPAHPIGHTVGFSNERAAYDMTNALLARGFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQEIRLGAPPLSIEDGVAAAELILQEYPDTDCIFCVSDMPAFGLLSRLKSIGVAVPEQVSVVGFGNFEVSRFASPEISTVRVDPIAIGRETGSLILRLLDPKQRSPQTAQHITLPPVLEFRPSLKNL 346
               SCOP domains d3e3ma_ A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.........eeee.hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.......eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhh.--------..eee...eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3m A  69 GFVGLLLPSLNNLHFAQTAQSLTDVLEQGGLQLLLGYTAYSPEREEQLVETMLRRRPEAMVLSYDGHTEQTIRLLQRASIPIVEIWEKPAHPIGHTVGFSNERAAYDMTNALLARGFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQEIRLGAPPLSIEDGVAAAELILQEYPDTDCIFCVSDMPAFGLLSRLKSIGVAVPEQVSVVGFGNFEVSRFASPEISTVRVDPIAIGRETGSLILRLLD--------AQHITLPPVLEFRPSLKNE 346
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318|      328       338        
                                                                                                                                                                                                                                                                                    319      328                  


Chain B from PDB  Type:PROTEIN  Length:270
 aligned with Q5LKY7_RUEPO | Q5LKY7 from UniProtKB/TrEMBL  Length:346

    Alignment length:278
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338        
         Q5LKY7_RUEPO    69 GFVGLLLPSLNNLHFAQTAQSLTDVLEQGGLQLLLGYTAYSPEREEQLVETMLRRRPEAMVLSYDGHTEQTIRLLQRASIPIVEIWEKPAHPIGHTVGFSNERAAYDMTNALLARGFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQEIRLGAPPLSIEDGVAAAELILQEYPDTDCIFCVSDMPAFGLLSRLKSIGVAVPEQVSVVGFGNFEVSRFASPEISTVRVDPIAIGRETGSLILRLLDPKQRSPQTAQHITLPPVLEFRPSLKNL 346
               SCOP domains d3e3mb_ B: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh....eeee.........eeee.hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.......eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhhh--------..eee...eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3m B  69 GFVGLLLPSLNNLHFAQTAQSLTDVLEQGGLQLLLGYTAYSPEREEQLVETMLRRRPEAMVLSYDGHTEQTIRLLQRASIPIVEIWEKPAHPIGHTVGFSNERAAYDMTNALLARGFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQEIRLGAPPLSIEDGVAAAELILQEYPDTDCIFCVSDMPAFGLLSRLKSIGVAVPEQVSVVGFGNFEVSRFASPEISTVRVDPIAIGRETGSLILRLLD--------AQHITLPPVLEFRPSLKNE 346
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318|      328       338        
                                                                                                                                                                                                                                                                                    319      328                  


Chain C from PDB  Type:PROTEIN  Length:270
 aligned with Q5LKY7_RUEPO | Q5LKY7 from UniProtKB/TrEMBL  Length:346

    Alignment length:278
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338        
         Q5LKY7_RUEPO    69 GFVGLLLPSLNNLHFAQTAQSLTDVLEQGGLQLLLGYTAYSPEREEQLVETMLRRRPEAMVLSYDGHTEQTIRLLQRASIPIVEIWEKPAHPIGHTVGFSNERAAYDMTNALLARGFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQEIRLGAPPLSIEDGVAAAELILQEYPDTDCIFCVSDMPAFGLLSRLKSIGVAVPEQVSVVGFGNFEVSRFASPEISTVRVDPIAIGRETGSLILRLLDPKQRSPQTAQHITLPPVLEFRPSLKNL 346
               SCOP domains d3e3mc_ C: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh....eeee.........eeee.hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.......eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhhh--------..eee...eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3m C  69 GFVGLLLPSLNNLHFAQTAQSLTDVLEQGGLQLLLGYTAYSPEREEQLVETMLRRRPEAMVLSYDGHTEQTIRLLQRASIPIVEIWEKPAHPIGHTVGFSNERAAYDMTNALLARGFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQEIRLGAPPLSIEDGVAAAELILQEYPDTDCIFCVSDMPAFGLLSRLKSIGVAVPEQVSVVGFGNFEVSRFASPEISTVRVDPIAIGRETGSLILRLLD--------AQHITLPPVLEFRPSLKNE 346
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318|      328       338        
                                                                                                                                                                                                                                                                                    319      328                  


Chain D from PDB  Type:PROTEIN  Length:270
 aligned with Q5LKY7_RUEPO | Q5LKY7 from UniProtKB/TrEMBL  Length:346

    Alignment length:278
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338        
         Q5LKY7_RUEPO    69 GFVGLLLPSLNNLHFAQTAQSLTDVLEQGGLQLLLGYTAYSPEREEQLVETMLRRRPEAMVLSYDGHTEQTIRLLQRASIPIVEIWEKPAHPIGHTVGFSNERAAYDMTNALLARGFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQEIRLGAPPLSIEDGVAAAELILQEYPDTDCIFCVSDMPAFGLLSRLKSIGVAVPEQVSVVGFGNFEVSRFASPEISTVRVDPIAIGRETGSLILRLLDPKQRSPQTAQHITLPPVLEFRPSLKNL 346
               SCOP domains d3e3md_ D: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh....eeee.........eeee.hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.......eee....hhhhhhh.....eee.hhhhhhhhhhhhhhhhh.--------..eee...eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3m D  69 GFVGLLLPSLNNLHFAQTAQSLTDVLEQGGLQLLLGYTAYSPEREEQLVETMLRRRPEAMVLSYDGHTEQTIRLLQRASIPIVEIWEKPAHPIGHTVGFSNERAAYDMTNALLARGFRKIVFLGEKDDDWTRGAARRAGFKRAMREAGLNPDQEIRLGAPPLSIEDGVAAAELILQEYPDTDCIFCVSDMPAFGLLSRLKSIGVAVPEQVSVVGFGNFEVSRFASPEISTVRVDPIAIGRETGSLILRLLD--------AQHITLPPVLEFRPSLKNE 346
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318|      328       338        
                                                                                                                                                                                                                                                                                    319      328
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E3M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E3M)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5LKY7_RUEPO | Q5LKY7)
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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  Cis Peptide Bonds
    Pro A:228 - Pro A:229   [ RasMol ]  
    Pro B:228 - Pro B:229   [ RasMol ]  
    Pro C:228 - Pro C:229   [ RasMol ]  
    Pro D:228 - Pro D:229   [ RasMol ]  
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    Ser B:293 - Pro B:294   [ RasMol ]  
    Ser C:293 - Pro C:294   [ RasMol ]  
    Ser D:293 - Pro D:294   [ RasMol ]  
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    Val B:274 - Pro B:275   [ RasMol ]  
    Val C:274 - Pro C:275   [ RasMol ]  
    Val D:274 - Pro D:275   [ RasMol ]  
 
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  3e3m
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