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(-) Description

Title :  DNA COMPLEXED STRUCTURE OF THE KEY TRANSCRIPTION FACTOR INITIATING DEVELOPMENT IN SPORULATION BACTERIA
 
Authors :  H. Zhao, T. Msadek, J. Zapf, Madhusudan, J. A. Hoch, K. I. Varughese
Date :  08 May 02  (Deposition) - 23 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  C,D,E,F  (1x)
Biol. Unit 2:  A,B,G,H  (1x)
Keywords :  Spo0A, Transcriptional Activation And Repression, 0A Box, Dna Complexed Structure, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zhao, T. Msadek, J. Zapf, Madhusudan, J. A. Hoch, K. I. Varughese
Dna Complexed Structure Of The Key Transcription Factor Initiating Development In Sporulating Bacteria.
Structure V. 10 1041 2002
PubMed-ID: 12176382  |  Reference-DOI: 10.1016/S0969-2126(02)00803-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3'
    Chains: E, G
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*AP*CP*AP*AP*AP*AP*TP*TP*CP*GP*AP*CP*AP*CP*GP*A)-3'
    Chains: F, H
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - STAGE 0 SPORULATION PROTEIN A
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: SPO0A
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: TRANSCRIPTION FACTOR SPO0A

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x):   CDEF  
Biological Unit 2 (1x): AB    GH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1LQ1)

(-) Sites  (0, 0)

(no "Site" information available for 1LQ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LQ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 1LQ1)

(-) 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:107
 aligned with SP0A_BACSU | P06534 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:115
                                   159       169       179       189       199       209       219       229       239       249       259     
           SP0A_BACSU   150 KKNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASRVERAIRHAIEVAWSRGNIDSISSLFGYTVSMTKAKPTNSEFIAMVADKLRLEH 264
               SCOP domains d1lq1a_ A: Spo0A                                                                                                    SCOP domains
               CATH domains 1lq1A00 A:150-264 'winged helix' repressor DNA binding domain                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhh--------...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1lq1 A 150 KKNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASRVERAIRHAIEVAWSRGNIDSISSLF--------AKPTNSEFIAMVADKLRLEH 264
                                   159       169       179       189       199       209       219       229      |  -     | 249       259     
                                                                                                                236      245                   


Chain B from PDB  Type:PROTEIN  Length:103
 aligned with SP0A_BACSU | P06534 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:111
                                   161       171       181       191       201       211       221       231       241       251       261 
           SP0A_BACSU   152 NLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASRVERAIRHAIEVAWSRGNIDSISSLFGYTVSMTKAKPTNSEFIAMVADKLRL 262
               SCOP domains d1lq1b_ B: Spo0A                                                                                                SCOP domains
               CATH domains 1lq1B00 B:152-262 'winged helix' repressor DNA binding domain                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhh--------...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1lq1 B 152 NLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASRVERAIRHAIEVAWSRGNIDSISSLF--------AKPTNSEFIAMVADKLRL 262
                                   161       171       181       191       201       211       221       231    |    -   |   251       261 
                                                                                                              236      245                 


Chain C from PDB  Type:PROTEIN  Length:112
 aligned with SP0A_BACSU | P06534 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:116
                                   160       170       180       190       200       210       220       230       240       250       260      
           SP0A_BACSU   151 KNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASRVERAIRHAIEVAWSRGNIDSISSLFGYTVSMTKAKPTNSEFIAMVADKLRLEHKA 266
               SCOP domains d1lq1c_ C: Spo0A                                                                                                     SCOP domains
               CATH domains 1lq1C00 C:151-266 'winged helix' repressor DNA binding domain                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....----....hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1lq1 C 151 KNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASRVERAIRHAIEVAWSRGNIDSISSLFGYT----KAKPTNSEFIAMVADKLRLEHKA 266
                                   160       170       180       190       200       210       220       230        |-   |   250       260      
                                                                                                                  239  244                      


Chain D from PDB  Type:PROTEIN  Length:107
 aligned with SP0A_BACSU | P06534 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:114
                                   160       170       180       190       200       210       220       230       240       250       260    
           SP0A_BACSU   151 KNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASRVERAIRHAIEVAWSRGNIDSISSLFGYTVSMTKAKPTNSEFIAMVADKLRLEH 264
               SCOP domains d1lq1d_ D: Spo0A                                                                                                   SCOP domains
               CATH domains 1lq1D00 D:151-264 'winged helix' repressor DNA binding domain                                                      CATH domains
           Pfam domains (1) -----Spo0A_C-1lq1D01 D:156-261                                                                                 --- Pfam domains (1)
           Pfam domains (2) -----Spo0A_C-1lq1D02 D:156-261                                                                                 --- Pfam domains (2)
           Pfam domains (3) -----Spo0A_C-1lq1D03 D:156-261                                                                                 --- Pfam domains (3)
           Pfam domains (4) -----Spo0A_C-1lq1D04 D:156-261                                                                                 --- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhh.-------....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1lq1 D 151 KNLDASITSIIHEIGVPAHIKGYLYLREAISMVYNDIELLGSITKVLYPDIAKKFNTTASRVERAIRHAIEVAWSRGNIDSISSLF-------KAKPTNSEFIAMVADKLRLEH 264
                                   160       170       180       190       200       210       220       230     |   -   |   250       260    
                                                                                                               236     244                    


Chain E from PDB  Type:DNA  Length:16
                                                
                 1lq1 E   1 TTCGTGTCGAATTTTG  16
                                    10      


Chain F from PDB  Type:DNA  Length:16
                                                
                 1lq1 F 115 ACAAAATTCGACACGA 130
                                   124      


Chain G from PDB  Type:DNA  Length:16
                                                
                 1lq1 G   1 TTCGTGTCGAATTTTG  16
                                    10      


Chain H from PDB  Type:DNA  Length:16
                                                
                 1lq1 H 115 ACAAAATTCGACACGA 130
                                   124
   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: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Spo0A_C] (1)
(-)
Family: Spo0A_C (1)
(-)
Bacillus subtilis (1)
1aSpo0A_C-1lq1D01D:156-261
1bSpo0A_C-1lq1D02D:156-261
1cSpo0A_C-1lq1D03D:156-261
1dSpo0A_C-1lq1D04D:156-261

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SP0A_BACSU | P06534)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008356    asymmetric cell division    The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity.
    GO:0000917    barrier septum assembly    The assembly and arrangement of a septum that spans the plasma membrane interface between progeny cells following cytokinesis. The progeny cells that form a barrier septum are not able to exchange intracellular material.
    GO:0051606    detection of stimulus    The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.
    GO:0032022    multicellular pellicle formation    A process in which microorganisms produce an extracellular matrix and form multicellular aggregates at an air-liquid interface.
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0045881    positive regulation of sporulation resulting in formation of a cellular spore    Any process that activates or increases the frequency, rate or extent of sporulation.
    GO:0043937    regulation of sporulation    Any process that modulates the frequency, rate or extent of sporulation, the process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure.
    GO:0042173    regulation of sporulation resulting in formation of a cellular spore    Any process that modulates the frequency, rate or extent of spore formation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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