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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOSPHORYLATED RECEIVER DOMAIN OF THE TRANSCRIPTION REGULATOR NTRC1 FROM AQUIFEX AEOLICUS
 
Authors :  M. Doucleff, B. Chen, A. E. Maris, D. E. Wemmer, E. Kondrashkina, B. T. Nixon
Date :  09 Jun 05  (Deposition) - 16 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.03
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphorylated Receiver Domain, Sigma-54 Activator, Two- Component Signaling, Ntrc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Doucleff, B. Chen, A. E. Maris, D. E. Wemmer, E. Kondrashkina, B. T. Nixon
Negative Regulation Of Aaa + Atpase Assembly By Two Component Receiver Domains: A Transcription Activation Mechanism That Is Conserved In Mesophilic And Extremely Hyperthermophilic Bacteria
J. Mol. Biol. V. 353 242 2005
PubMed-ID: 16169010  |  Reference-DOI: 10.1016/J.JMB.2005.08.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR NTRC1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21/DE3 WITH ROSETTA PLYS PLASMID
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NTRC1
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: NTRC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PHD2Mod. Amino AcidASPARTYL PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , PHD A:51 , LEU A:53BINDING SITE FOR RESIDUE MG A 151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZY2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:101 -Pro A:102
2Lys B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZY2)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZY2)

(-) Sequences/Alignments

Asymmetric/Biological 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:140
 aligned with O67198_AQUAE | O67198 from UniProtKB/TrEMBL  Length:439

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         O67198_AQUAE     1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKENELLRREKDLKEEEYVFESPKMKEILEKIKKISC 158
               SCOP domains d1zy2a1 A:1-136 Transcriptional activator sigm54 (NtrC1), N-terminal domain                                                             ---------------------- SCOP domains
               CATH domains 1zy2A00 A:1-140  [code=3.40.50.2300, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh.eee...hhhhhhhhh......eeeee......hhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh------------------hh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zy2 A   1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLdLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKENELLRREKDLKE------------------KLAA 140
                                    10        20        30        40        50|       60        70        80        90       100       110       120       130     |   -         -    |   
                                                                             51-PHD                                                                              136                137   


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with O67198_AQUAE | O67198 from UniProtKB/TrEMBL  Length:439

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
         O67198_AQUAE     1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKEN 125
               SCOP domains d1zy2b_ B: Transcriptional activator sigm54 (NtrC1), N-terminal domain                                                        SCOP domains
               CATH domains 1zy2B00 B:1-125  [code=3.40.50.2300, no name defined]                                                                         CATH domains
           Pfam domains (1) --Response_reg-1zy2B01 B:3-113                                                                                   ------------ Pfam domains (1)
           Pfam domains (2) --Response_reg-1zy2B02 B:3-113                                                                                   ------------ Pfam domains (2)
         Sec.struct. author .eeee...hhhhhhhhhhhhhhhh.eee...hhhhhhhhhhhh...eee.........hhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zy2 B   1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLdLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKEN 125
                                    10        20        30        40        50|       60        70        80        90       100       110       120     
                                                                             51-PHD
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: CheY (97)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O67198_AQUAE | O67198)
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

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UniProtKB/TrEMBL
        O67198_AQUAE | O67198: 1ny5 1ny6 3m0e 4bs1 4bt0 4bt1 4l4u 4l5e 4ly6 4lzz

(-) Related Entries Specified in the PDB File

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