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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RECEIVER DOMAIN AND LINKER REGION OF DCTD FROM SINORHIZOBIUM MELILOTI
 
Authors :  M. G. Meyer, S. Park, L. Zeringue, M. Staley, M. Mckinstry, R. I. Kaufman, H. Zhang, D. Yan, N. Yennawar, G. K. Farber, B. T. Nixon
Date :  23 Jul 99  (Deposition) - 30 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transcriptional Regulatory Protein, Receiver Domain, 2-Component Signal Transduction, Sigma-54 Dependent Transcriptional Activator, Bacterial Enhancer Binding Protein, High Solvent Content Crystal (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Meyer, S. Park, L. Zeringue, M. Staley, M. Mckinstry, R. I. Kaufman, H. Zhang, D. Yan, N. Yennawar, G. K. Farber, B. T. Nixon
A Dimeric Two-Component Receiver Domain Inhibits The Sigma54-Dependent Atpase In Dctd
Faseb J. V. 15 1326 2001
PubMed-ID: 11344129
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Variant: B834 PLYSS
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2 TO 143, RECEIVER DOMAIN
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 382
    Other Details: THE PROTEIN WAS EXPRESSED WITH THE C-TERMINAL HIS-TAG, KLAAALEHHHHHH. COORDINATES ARE SUBMITTED ONLY FOR THE MONOMER, WHICH COMPRISES THE COMPLETE ASYMMETRIC UNIT.
    Plasmid: PT143WT
    Strain: N.A. 1021
    Synonym: DCTD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1QKK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:105 -Pro A:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RESPONSE_REGULATORYPS50110 Response regulatory domain profile.DCTD_RHIME6-120  1A:6-120
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RESPONSE_REGULATORYPS50110 Response regulatory domain profile.DCTD_RHIME6-120  2A:6-120

(-) Exons   (0, 0)

(no "Exon" information available for 1QKK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:140
 aligned with DCTD_RHIME | P13632 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:140
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144
           DCTD_RHIME     5 PSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLVMENRSLRRAAEAASEGLP 144
               SCOP domains d1qkka_ A: Transcriptional regulatory protein DctD, receiver domain                                                                          SCOP domains
               CATH domains 1qkkA00 A:5-144  [code=3.40.50.2300, no name defined]                                                                                        CATH domains
               Pfam domains --Response_reg-1qkkA01 A:7-117                                                                                   --------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhh.......eeeee......hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: A:6-120 UniProt: 6-120                                                                   ------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qkk A   5 PSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLVMENRSLRRAAEAASEGLK 144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: CheY (97)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (DCTD_RHIME | P13632)
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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    Lys A:105 - Pro A:106   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCTD_RHIME | P13632: 1l5y 1l5z

(-) Related Entries Specified in the PDB File

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