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(-) Description

Title :  MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE SITE CONTACTS
 
Authors :  C. A. Hastings, S. -Y. Lee, H. S. Cho, D. Yan, S. Kustu, D. E. Wemmer
Date :  10 Jan 02  (Deposition) - 19 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Two Component Signal Transduction, Receiver Domain, Bef3, Phosphorylation, Bacterial Nitrogen Regulatory Protein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Hastings, S. -Y. Lee, H. S. Cho, D. Yan, S. Kustu, D. E. Wemmer
High-Resolution Solution Structure Of The Beryllofluoride-Activated Ntrc Receiver Domain
Biochemistry V. 42 9081 2003
PubMed-ID: 12885241  |  Reference-DOI: 10.1021/BI0273866
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITROGEN REGULATION PROTEIN NR(I)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:54 , ILE A:55 , ARG A:56 , THR A:82 , HIS A:84 , LYS A:104BINDING SITE FOR RESIDUE BEF A 125

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J56)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J56)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J56)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RESPONSE_REGULATORYPS50110 Response regulatory domain profile.NTRC_SALTY5-119  1A:5-119

(-) Exons   (0, 0)

(no "Exon" information available for 1J56)

(-) Sequences/Alignments

NMR Structure
   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:124
 aligned with NTRC_SALTY | P41789 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
           NTRC_SALTY     1 MQRGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQE 124
               SCOP domains d1j56a_ A: NTRC receiver domain                                                                                              SCOP domains
               CATH domains 1j56A00 A:1-124  [code=3.40.50.2300, no name defined]                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhhh.eeeee..hhhhhhhh......eeee.........hhhhhhhhhhh....eee.....hhhhhhhhhhhh..ee......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RESPONSE_REGULATORY  PDB: A:5-119 UniProt: 5-119                                                                   ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j56 A   1 MQRGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQE 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
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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)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J56)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (NTRC_SALTY | P41789)
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:0000156    phosphorelay response regulator activity    Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
    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:0009399    nitrogen fixation    The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
    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:0006808    regulation of nitrogen utilization    Any process that modulates the frequency, rate or extent of nitrogen utilization.
    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/Swiss-Prot
        NTRC_SALTY | P41789: 1dc7 1dc8 1krw 1krx 1ntc 1ntr

(-) Related Entries Specified in the PDB File

1dc7 INACTIVE CONFORMATION OF NTRC RECEIVER DOMAIN
1dc8 TRANSIENTLY PHOSPHORYLATED FORM OF NTRC RECEIVER DOMAIN
1djm SOLUTION STRUCTURE OF ACTIVE CHEY, THE HOMOLOG OF NTRC RECEIVER DOMAIN
1f4v CRYSTAL STRUCTURE OF ACTIVE CHEY BOUND TO ITS DOWNSTREAM TARGET DOMAIN
1krw SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF BERYLLOFLUORIDE -ACTIVATED NTRC RECEIVER DOMAIN
1krx SOLUTION STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURES INCORPORATING ACTIVE SITE CONTACTS