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(-) Description

Title :  STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DNAA-DBD IN COMPLEX WITH BOX1 DNA
 
Authors :  O. V. Tsodikov, T. Biswas
Date :  07 Dec 10  (Deposition) - 25 May 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Helix-Turn-Helix Motif, Interacting With Dnaa-Box, Dnaa-Box, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. V. Tsodikov, T. Biswas
Structural And Thermodynamic Signatures Of Dna Recognition By Mycobacterium Tuberculosis Dnaa.
J. Mol. Biol. V. 410 461 2011
PubMed-ID: 21620858  |  Reference-DOI: 10.1016/J.JMB.2011.05.007

(-) Compounds

Molecule 1 - CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19PPS
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNAA DBD
    Gene: DNAA, MRA_0001, RV0001
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 419947
    Strain: ATCC 25177 / H37RA
 
Molecule 2 - DNA (5'-D(*CP*GP*TP*TP*GP*TP*CP*CP*AP*CP*AP*AP*C)-3')
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*CP*AP*AP*CP*G)-3')
    Chains: D, F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3PVV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNAAPS01008 DnaA protein signature.DNAA_MYCTA462-480
 		  2A:462-480
B:462-480
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNAAPS01008 DnaA protein signature.DNAA_MYCTA462-480
 		  1A:462-480
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNAAPS01008 DnaA protein signature.DNAA_MYCTA462-480
 		  1-
B:462-480

(-) Exons   (0, 0)

(no "Exon" information available for 3PVV)

(-) 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:96
 aligned with DNAA_MYCTA | A5TY69 from UniProtKB/Swiss-Prot  Length:507

    Alignment length:96
                                   420       430       440       450       460       470       480       490       500      
           DNAA_MYCTA   411 ISAATIMAATAEYFDTTVEELRGPGKTRALAQSRQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEMAERREVFDHVKELTTRIRQRSK 506
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------DNAA  PDB: A:462-48-------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3pvv A 411 ISAATIMAATAEYFDTTVEELRGPGKTRALAQSRQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEMAERREVFDHVKELTTRIRQRSK 506
                                   420       430       440       450       460       470       480       490       500      


Chain B from PDB  Type:PROTEIN  Length:95
 aligned with DNAA_MYCTA | A5TY69 from UniProtKB/Swiss-Prot  Length:507

    Alignment length:95
                                   420       430       440       450       460       470       480       490       500     
           DNAA_MYCTA   411 ISAATIMAATAEYFDTTVEELRGPGKTRALAQSRQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEMAERREVFDHVKELTTRIRQRS 505
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Bac_DnaA_C-3pvvB01 B:412-480                                         ------------------------- Pfam domains (1)
           Pfam domains (2) -Bac_DnaA_C-3pvvB02 B:412-480                                         ------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------DNAA  PDB: B:462-48------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 3pvv B 411 ISAATIMAATAEYFDTTVEELRGPGKTRALAQSRQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEMAERREVFDHVKELTTRIRQRS 505
                                   420       430       440       450       460       470       480       490       500     


Chain C from PDB  Type:DNA  Length:13
                                             
                 3pvv C 101 CGTTGTCCACAAC 113
                                   110   


Chain D from PDB  Type:DNA  Length:13
                                             
                 3pvv D 201 GTTGTGGACAACG 213
                                   210   


Chain E from PDB  Type:DNA  Length:13
                                             
                 3pvv E 101 CGTTGTCCACAAC 113
                                   110   


Chain F from PDB  Type:DNA  Length:13
                                             
                 3pvv F 201 GTTGTGGACAACG 213
                                   210
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DNAA_MYCTA | A5TY69)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
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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 Related Entries

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        DNAA_MYCTA | A5TY69: 3pvp

(-) Related Entries Specified in the PDB File

3pvp