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(-) Description

Title :  CRYSTAL STRUCTURE OF SIGMA54 ACTIVATOR NTRC4'S DNA BINDING DOMAIN
 
Authors :  J. D. Batchelor, M. Doucleff, C. -J. Lee, K. Matsubara, S. De Carlo, J. Heideker, M. M. Lamers, J. G. Pelton, D. E. Wemmer
Date :  18 Aug 08  (Deposition) - 25 Nov 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Sigma43 Activator, Aaa+ Atpase, Response Regulator, Transcriptional Activator, Atp-Binding, Nucleotide-Binding, Transcription, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Batchelor, M. Doucleff, C. J. Lee, K. Matsubara, S. De Carlo, J. Heideker, M. H. Lamers, J. G. Pelton, D. E. Wemmer
Structure And Regulatory Mechanism Of Aquifex Aeolicus Ntrc4: Variability And Evolution In Bacterial Transcriptional Regulation.
J. Mol. Biol. V. 384 1058 2008
PubMed-ID: 18955063  |  Reference-DOI: 10.1016/J.JMB.2008.10.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR (NTRC FAMILY)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSKB3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 380 TO 442
    Gene: NTRC4, AQ_164
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:57 , SER D:79BINDING SITE FOR RESIDUE ZN A 2
2AC2SOFTWAREGLU B:57BINDING SITE FOR RESIDUE ZN B 3
3AC3SOFTWAREGLU B:27 , ASP D:48BINDING SITE FOR RESIDUE ZN B 4
4AC4SOFTWAREASP A:50 , GLU C:27 , GLU C:30BINDING SITE FOR RESIDUE ZN C 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E7L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg D:17 -Asp D:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E7L)

(-) Exons   (0, 0)

(no "Exon" information available for 3E7L)

(-) 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:60
 aligned with O66551_AQUAE | O66551 from UniProtKB/TrEMBL  Length:442

    Alignment length:60
                                   392       402       412       422       432       442
         O66551_AQUAE   383 SYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRVKSS 442
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 3e7l A  20 SYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRVKSS  79
                                    29        39        49        59        69        79


Chain B from PDB  Type:PROTEIN  Length:54
 aligned with O66551_AQUAE | O66551 from UniProtKB/TrEMBL  Length:442

    Alignment length:54
                                   392       402       412       422       432    
         O66551_AQUAE   383 SYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLN 436
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 3e7l B  20 SYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLN  73
                                    29        39        49        59        69    


Chain C from PDB  Type:PROTEIN  Length:60
 aligned with O66551_AQUAE | O66551 from UniProtKB/TrEMBL  Length:442

    Alignment length:60
                                   389       399       409       419       429       439
         O66551_AQUAE   380 RDLSYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRV 439
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 3e7l C  17 RDLSYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRV  76
                                    26        36        46        56        66        76


Chain D from PDB  Type:PROTEIN  Length:63
 aligned with O66551_AQUAE | O66551 from UniProtKB/TrEMBL  Length:442

    Alignment length:63
                                   389       399       409       419       429       439   
         O66551_AQUAE   380 RDLSYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRVKSS 442
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 3e7l D  17 RDLSYLLKIKELKEAKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRVKSS  79
                                    26        36        46        56        66        76
   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 3E7L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E7L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E7L)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O66551_AQUAE | O66551)
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: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.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    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: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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/TrEMBL
        O66551_AQUAE | O66551: 1zit 2jrl 3dzd 4fth

(-) Related Entries Specified in the PDB File

3dzd