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(-) Description

Title :  NARL COMPLEXED TO NIRB PROMOTER NON-PALINDROMIC TAIL-TO-TAIL DNA SITE
 
Authors :  A. E. Maris, M. Kaczor-Grzeskowiak, Z. Ma, M. L. Kopka, R. P. Gunsalus, R. E. Dickerson
Date :  20 Apr 05  (Deposition) - 22 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Protein-Dna Complex, Helix-Turn-Helix, Two-Component Response Regulator, Dna Bending, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. E. Maris, M. Kaczor-Grzeskowiak, Z. Ma, M. L. Kopka, R. P. Gunsalus, R. E. Dickerson
Primary And Secondary Modes Of Dna Recognition By The Narl Two-Component Response Regulator.
Biochemistry V. 44 14538 2005
PubMed-ID: 16262254  |  Reference-DOI: 10.1021/BI050734U
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*CP*GP*TP*AP*CP*TP*CP*CP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP *G)-3'
    Chains: C, H
    Engineered: YES
    Other Details: SOLID PHASE SYNTHESIS
    Synthetic: YES
 
Molecule 2 - 5'- D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*GP*GP*AP*GP*TP*AP*CP *G)-3'
    Chains: D, G
    Engineered: YES
    Other Details: SOLID PHASE SYNTHESIS
    Synthetic: YES
 
Molecule 3 - NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMJ05
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN (RESIDUES 147-216)
    Gene: NARL, FRDR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2SO49Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:72 , SER A:185 , LYS A:188 , HOH C:312 , DC D:26BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARESER B:185 , LYS B:188 , DT C:6 , DC C:7 , HOH C:311BINDING SITE FOR RESIDUE SO4 C 302
3AC3SOFTWARESER E:185 , LYS E:188 , HOH G:309 , HOH G:311 , DT H:26 , DC H:27BINDING SITE FOR RESIDUE SO4 H 303
4AC4SOFTWARESER F:185 , DC G:6 , DC G:7 , HOH H:313BINDING SITE FOR RESIDUE SO4 G 304
5AC5SOFTWAREPRO A:158 , ARG A:161BINDING SITE FOR RESIDUE SO4 A 305
6AC6SOFTWAREPRO B:158 , ARG B:161BINDING SITE FOR RESIDUE SO4 B 306
7AC7SOFTWAREPRO E:158 , ARG E:161BINDING SITE FOR RESIDUE SO4 E 307
8AC8SOFTWAREPRO F:158 , ARG F:161BINDING SITE FOR RESIDUE SO4 F 308
9AC9SOFTWAREARG B:178BINDING SITE FOR RESIDUE SO4 B 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZG1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZG1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZG1)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LUXR_1PS00622 LuxR-type HTH domain signature.NARL_ECOLI170-197
 
 
 		  4A:170-197
B:170-197
E:170-197
F:170-197
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LUXR_1PS00622 LuxR-type HTH domain signature.NARL_ECOLI170-197
 
 
 		  2A:170-197
B:170-197
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LUXR_1PS00622 LuxR-type HTH domain signature.NARL_ECOLI170-197
 
 
 		  2-
-
E:170-197
F:170-197

(-) Exons   (0, 0)

(no "Exon" information available for 1ZG1)

(-) 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:66
 aligned with NARL_ECOLI | P0AF28 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:66
                                   160       170       180       190       200       210      
           NARL_ECOLI   151 RDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF 216
               SCOP domains d1zg1a1 A:151-216 Nitrate/nitrite response regulator (NarL)        SCOP domains
               CATH domains 1zg1A00 A:151-216 'winged helix' repressor DNA binding domain      CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------HTH_LUXR_1  PDB: A:170-197  ------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 1zg1 A 151 RDVNQLTPRERDILKLIAQGLPNKmIARRLDITESTVKVHVKHmLKKmKLKSRVEAAVWVHQERIF 216
                                   160       170    |  180       190   |   200       210      
                                                  175-MSE            194-MSE                  
                                                                         198-MSE              


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with NARL_ECOLI | P0AF28 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:66
                                   160       170       180       190       200       210      
           NARL_ECOLI   151 RDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF 216
               SCOP domains d1zg1b1 B:151-216 Nitrate/nitrite response regulator (NarL)        SCOP domains
               CATH domains 1zg1B00 B:151-216 'winged helix' repressor DNA binding domain      CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------HTH_LUXR_1  PDB: B:170-197  ------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 1zg1 B 151 RDVNQLTPRERDILKLIAQGLPNKmIARRLDITESTVKVHVKHmLKKmKLKSRVEAAVWVHQERIF 216
                                   160       170    |  180       190   |   200       210      
                                                  175-MSE            194-MSE                  
                                                                         198-MSE              


Chain C from PDB  Type:DNA  Length:20
                                                    
                 1zg1 C   1 CGTACTCCTTAATGGGTACG  20
                                    10        20


Chain D from PDB  Type:DNA  Length:20
                                                    
                 1zg1 D  21 CGTACCCATTAAGGAGTACG  40
                                    30        40


Chain E from PDB  Type:PROTEIN  Length:66
 aligned with NARL_ECOLI | P0AF28 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:66
                                   160       170       180       190       200       210      
           NARL_ECOLI   151 RDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF 216
               SCOP domains d1zg1e1 E:151-216 Nitrate/nitrite response regulator (NarL)        SCOP domains
               CATH domains 1zg1E00 E:151-216 'winged helix' repressor DNA binding domain      CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------HTH_LUXR_1  PDB: E:170-197  ------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 1zg1 E 151 RDVNQLTPRERDILKLIAQGLPNKmIARRLDITESTVKVHVKHmLKKmKLKSRVEAAVWVHQERIF 216
                                   160       170    |  180       190   |   200       210      
                                                  175-MSE            194-MSE                  
                                                                         198-MSE              


Chain F from PDB  Type:PROTEIN  Length:66
 aligned with NARL_ECOLI | P0AF28 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:66
                                   160       170       180       190       200       210      
           NARL_ECOLI   151 RDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF 216
               SCOP domains d1zg1f1 F:151-216 Nitrate/nitrite response regulator (NarL)        SCOP domains
               CATH domains 1zg1F00 F:151-216 'winged helix' repressor DNA binding domain      CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------HTH_LUXR_1  PDB: F:170-197  ------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 1zg1 F 151 RDVNQLTPRERDILKLIAQGLPNKmIARRLDITESTVKVHVKHmLKKmKLKSRVEAAVWVHQERIF 216
                                   160       170    |  180       190   |   200       210      
                                                  175-MSE            194-MSE                  
                                                                         198-MSE              


Chain G from PDB  Type:DNA  Length:20
                                                    
                 1zg1 G   1 CGTACCCATTAAGGAGTACG  20
                                    10        20


Chain H from PDB  Type:DNA  Length:20
                                                    
                 1zg1 H  21 CGTACTCCTTAATGGGTACG  40
                                    30        40
   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, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZG1)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,E,F   (NARL_ECOLI | P0AF28)
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.
biological process
    GO:0042128    nitrate assimilation    The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
    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:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0090352    regulation of nitrate assimilation    Any process that modulates the rate, frequency, or extent of the uptake, from the environment, of nitrates, inorganic or organic salts and esters of nitric acid and the subsequent reduction of nitrate ion to other, less highly oxidized, inorganic nitrogenous substances.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NARL_ECOLI | P0AF28: 1a04 1je8 1rnl 1zg5

(-) Related Entries Specified in the PDB File

1a04 FULL-LENGTH UNACTIVATED NARL
1je8 NARL-DNA COMPLEX OF NIRB PALINDROME
1rnl FULL-LENGTH UNACTIVATED NARL
1zg5