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(-) Description

Title :  DNA BINDING DOMAIN OF THE PHAGE T4 TRANSCRIPTION FACTOR MOTA (AA105-211)
 
Authors :  N. Li, E. A. Sickmier, R. Zhang, A. Joachimiak, S. W. White
Date :  01 Nov 01  (Deposition) - 21 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Escherichia Coli; X-Ray Crystallography; Protein-Dna Interactions; Structural Genomics; Eubacterial Promoters. , Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Li, E. A. Sickmier, R. Zhang, A. Joachimiak, S. W. White
The Mota Transcription Factor From Bacteriophage T4 Contains A Novel Dna-Binding Domain: The 'Double Wing' Motif.
Mol. Microbiol. V. 43 1079 2002
PubMed-ID: 11918797  |  Reference-DOI: 10.1046/J.1365-2958.2002.02809.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION REGULATORY PROTEIN MOTA
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET13A
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN RESIDUES 105-211
    Gene: MOTA
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1KAF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KAF)

(-) 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:108
 aligned with MOTA_BPT4 | P22915 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:108
                                   113       123       133       143       153       163       173       183       193       203        
            MOTA_BPT4   104 REITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
               SCOP domains d1kafa_ A: DNA-binding C-terminal domain of the transcription factor MotA                                    SCOP domains
               CATH domains 1kafA00 A:104-211 DNA-binding domain of the transcription factor MotA                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeee....eeeeeee..hhhhhhhhhh...eeee....eeeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1kaf A 104 MEITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
                                   113       123       133       143       153       163       173       183       193       203        


Chain B from PDB  Type:PROTEIN  Length:108
 aligned with MOTA_BPT4 | P22915 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:108
                                   113       123       133       143       153       163       173       183       193       203        
            MOTA_BPT4   104 REITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
               SCOP domains d1kafb_ B: DNA-binding C-terminal domain of the transcription factor MotA                                    SCOP domains
               CATH domains 1kafB00 B:104-211 DNA-binding domain of the transcription factor MotA                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeee....eeeeeee..hhhhhhhhhhh..eeee....eeeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1kaf B 104 MEITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
                                   113       123       133       143       153       163       173       183       193       203        


Chain C from PDB  Type:PROTEIN  Length:108
 aligned with MOTA_BPT4 | P22915 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:108
                                   113       123       133       143       153       163       173       183       193       203        
            MOTA_BPT4   104 REITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
               SCOP domains d1kafc_ C: DNA-binding C-terminal domain of the transcription factor MotA                                    SCOP domains
               CATH domains 1kafC00 C:104-211 DNA-binding domain of the transcription factor MotA                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeee....eeeeeee..hhhhhhhhhhh..eeee....eeeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1kaf C 104 MEITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
                                   113       123       133       143       153       163       173       183       193       203        


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with MOTA_BPT4 | P22915 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:104
                                   117       127       137       147       157       167       177       187       197       207    
            MOTA_BPT4   108 SDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
               SCOP domains d1kafd_ D: DNA-binding C-terminal domain of the transcription factor MotA                                SCOP domains
               CATH domains 1kafD00 D:108-211 DNA-binding domain of the transcription factor MotA                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeeee...eeeeeeeeee..eeeeeee...eeeeeee..hhhhhhhhhhh..eeee....eeeeeee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1kaf D 108 SDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
                                   117       127       137       147       157       167       177       187       197       207    


Chain E from PDB  Type:PROTEIN  Length:103
 aligned with MOTA_BPT4 | P22915 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:103
                                   118       128       138       148       158       168       178       188       198       208   
            MOTA_BPT4   109 DMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
               SCOP domains d1kafe_ E: DNA-binding C-terminal domain of the transcription factor MotA                               SCOP domains
               CATH domains 1kafE00 E:109-211 DNA-binding domain of the transcription factor MotA                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeeeee...eeeeeeeeee..eeeeeee...eeeeeee..hhhhhhhhhh...eeee....eeeeeee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1kaf E 109 DMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
                                   118       128       138       148       158       168       178       188       198       208   


Chain F from PDB  Type:PROTEIN  Length:104
 aligned with MOTA_BPT4 | P22915 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:104
                                   117       127       137       147       157       167       177       187       197       207    
            MOTA_BPT4   108 SDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
               SCOP domains d1kaff_ F: DNA-binding C-terminal domain of the transcription factor MotA                                SCOP domains
               CATH domains 1kafF00 F:108-211 DNA-binding domain of the transcription factor MotA                                    CATH domains
           Pfam domains (1) MotCF-1kafF01 F:108-208                                                                              --- Pfam domains (1)
           Pfam domains (2) MotCF-1kafF02 F:108-208                                                                              --- Pfam domains (2)
           Pfam domains (3) MotCF-1kafF03 F:108-208                                                                              --- Pfam domains (3)
           Pfam domains (4) MotCF-1kafF04 F:108-208                                                                              --- Pfam domains (4)
           Pfam domains (5) MotCF-1kafF05 F:108-208                                                                              --- Pfam domains (5)
           Pfam domains (6) MotCF-1kafF06 F:108-208                                                                              --- Pfam domains (6)
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeeee...eeeeeee..hhhhhhhhhhh..eeee....eeeeeee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1kaf F 108 SDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNNGNMRIFGYKMMEHHIQKFTDIGMSCKIAKNGNVYLDIKRSAENIEAVITVASEL 211
                                   117       127       137       147       157       167       177       187       197       207
   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, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: MotCF] (1)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (MOTA_BPT4 | P22915)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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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 Related Entries

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

UniProtKB/Swiss-Prot
        MOTA_BPT4 | P22915: 1bja 1i1s 5jlt

(-) Related Entries Specified in the PDB File

1bja ACTIVATION DOMAIN OF THE PHAGE T4 TRANSCRIPTION FACTOR MOTA
1i1s SOLUTION STRUCTURE OF THE TRANSCRIPTIONAL ACTIVATION DOMAIN OF THE BACTERIOPHAGE T4 PROTEIN MOTA