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(-) Description

Title :  CRYSTAL STRUCTURE OF NTCA IN COMPLEX WITH 2,2-DIFLUOROPENTANEDIOIC ACID
 
Authors :  M. X. Zhao, Y. L. Jiang, Y. X. He, Y. F. Chen, Y. B. Teng, Y. X. Chen, C. C. Zha C. Z. Zhou
Date :  06 Jan 10  (Deposition) - 14 Jul 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nitrogen Regulator, Activator, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. X. Zhao, Y. L. Jiang, Y. X. He, Y. F. Chen, Y. B. Teng, Y. X. Chen, C. C. Zhang, C. Z. Zhou
Structural Basis For The Allosteric Control Of The Global Transcription Factor Ntca By The Nitrogen Starvation Signal 2-Oxoglutarate.
Proc. Natl. Acad. Sci. Usa V. 107 12487 2010
PubMed-ID: 20616047  |  Reference-DOI: 10.1073/PNAS.1001556107

(-) Compounds

Molecule 1 - GLOBAL NITROGEN REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ALR4392, BIFA, NTCA
    Organism Scientific: ANABAENA
    Organism Taxid: 103690
    Strain: PCC 7120
    Synonym: DNA-BINDING PROTEIN VF1, NITROGEN-RESPONSIVE REGULATORY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
12FT2Ligand/Ion2,2-DIFLUOROPENTANEDIOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:35 , LEU A:54 , PHE A:75 , GLY A:76 , VAL A:77 , LEU A:78 , ARG A:88 , TYR A:90 , ARG A:129 , HOH A:229 , ILE B:130 , LEU B:131 , GLU B:134BINDING SITE FOR RESIDUE 2FT A 224
2AC2SOFTWAREGLU A:134 , PHE B:35 , LEU B:54 , PHE B:75 , GLY B:76 , VAL B:77 , LEU B:78 , ARG B:88 , ARG B:129 , HOH B:234BINDING SITE FOR RESIDUE 2FT B 224

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LA3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LA3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LA3)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.NTCA_NOSS128-129
 		  2A:28-129
B:28-129
2HTH_CRP_2PS51063 Crp-type HTH domain profile.NTCA_NOSS1143-216
 		  2A:143-216
B:143-216
3HTH_CRP_1PS00042 Crp-type HTH domain signature.NTCA_NOSS1174-197
 		  2A:174-197
B:174-197

(-) Exons   (0, 0)

(no "Exon" information available for 3LA3)

(-) 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:198
 aligned with NTCA_NOSS1 | P0A4U6 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:198
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
           NTCA_NOSS1    25 VETFERNKTIFFPGDPAERVYFLLKGAVKLSRVYEAGEEITVALLRENSVFGVLSLLTGNKSDRFYHAVAFTPVELLSAPIEQVEQALKENPELSMLMLRGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKKITVHKPVTLSRQF 222
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee....eee.......eeeeeee..eeeeee.....eeeeeee....eehhhhhhhhhhh....eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhh..hhhhhhhhhhhhhhh..eeee..eeee.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---CNMP_BINDING_3  PDB: A:28-129 UniProt: 28-129                                                         -------------HTH_CRP_2  PDB: A:143-216 UniProt: 143-216                                ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: A:174-19------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3la3 A  25 VETFERNKTIFFPGDPAERVYFLLKGAVKLSRVYEAGEEITVALLRENSVFGVLSLLTGNKSDRFYHAVAFTPVELLSAPIEQVEQALKENPELSMLMLRGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKKITVHKPVTLSRQF 222
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with NTCA_NOSS1 | P0A4U6 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:197
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
           NTCA_NOSS1    25 VETFERNKTIFFPGDPAERVYFLLKGAVKLSRVYEAGEEITVALLRENSVFGVLSLLTGNKSDRFYHAVAFTPVELLSAPIEQVEQALKENPELSMLMLRGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKKITVHKPVTLSRQ 221
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) cNMP_binding-3la3B03 B:25-117                                                                -----------------------------HTH_Crp_2-3la3B01 B:147-220                                               - Pfam domains (1)
           Pfam domains (2) cNMP_binding-3la3B04 B:25-117                                                                -----------------------------HTH_Crp_2-3la3B02 B:147-220                                               - Pfam domains (2)
         Sec.struct. author .eee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhhhhhhh....eeee...eeeeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CNMP_BINDING_3  PDB: B:28-129 UniProt: 28-129                                                         -------------HTH_CRP_2  PDB: B:143-216 UniProt: 143-216                                ----- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: B:174-19------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3la3 B  25 VETFERNKTIFFPGDPAERVYFLLKGAVKLSRVYEAGEEITVALLRENSVFGVLSLLTGNKSDRFYHAVAFTPVELLSAPIEQVEQALKENPELSMLMLRGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKKITVHKPVTLSRQ 221
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214
   Legend:   → Mismatch (orange background)
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  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 3LA3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LA3)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: no clan defined [family: cNMP_binding] (41)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NTCA_NOSS1 | P0A4U6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    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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  3la3
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 Related Entries

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

UniProtKB/Swiss-Prot
        NTCA_NOSS1 | P0A4U6: 3la2 3la7

(-) Related Entries Specified in the PDB File

3la2 3la7