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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR NTCA FROM SYNECHOCOCCUS ELONGATUS BOUND TO 2-OXOGLUTARATE
 
Authors :  J. L. Llacer, M. A. Castells, V. Rubio
Date :  17 Jun 10  (Deposition) - 18 Aug 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Nitrogen Assimilation, Crp/Fnr Superfamily, 2-Oxoglutarate, Global Nitrogen Controller. (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. L. Llacer, J. Espinosa, M. A. Castells, A. Contreras, K. Forchhammer, V. Rubio
Structural Basis For The Regulation Of Ntca- Dependent Transcription By Proteins Pipx And Pii.
Proc. Natl. Acad. Sci. Usa V. 107 15397 2010
PubMed-ID: 20716687  |  Reference-DOI: 10.1073/PNAS.1007015107

(-) Compounds

Molecule 1 - GLOBAL NITROGEN REGULATOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainROSETTA
    Expression System Taxid562
    Organism ScientificSYNECHOCOCCUS ELONGATUS
    Organism Taxid1140
    StrainPCC 7942
    SynonymNTCA

 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
1AKG2Ligand/Ion2-OXOGLUTARIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:53 , PHE A:74 , GLY A:75 , VAL A:76 , LEU A:77 , ARG A:87 , ARG A:128 , HOH A:2050 , ILE B:129 , GLU B:133BINDING SITE FOR RESIDUE AKG A 519
2AC2SOFTWAREILE A:129 , GLU A:133 , LEU B:53 , PHE B:74 , GLY B:75 , VAL B:76 , LEU B:77 , ARG B:87 , ARG B:128 , HOH B:2066BINDING SITE FOR RESIDUE AKG B 519

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XHK)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:81 -Gly A:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XHK)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.NTCA_SYNE722-128
 
  2A:22-128
B:22-128
2HTH_CRP_2PS51063 Crp-type HTH domain profile.NTCA_SYNE7142-215
 
  2A:142-215
B:142-215
3HTH_CRP_1PS00042 Crp-type HTH domain signature.NTCA_SYNE7173-196
 
  2A:173-196
B:173-196

(-) Exons   (0, 0)

(no "Exon" information available for 2XHK)

(-) 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:215
 aligned with NTCA_SYNE7 | P29283 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:218
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
           NTCA_SYNE7     5 ENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS 222
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..---.....eee...eeee.......eeeeeee.eeeeeeee...eeeeeeee..eeeehhhhhh.........eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeeehhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------CNMP_BINDING_3  PDB: A:22-128 UniProt: 22-128                                                              -------------HTH_CRP_2  PDB: A:142-215 UniProt: 142-215                                ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: A:173-19-------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhk A   5 ENSLLTMFRELG---LPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS 222
                                    14 |   |  24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
                                      16  20                                                                                                                                                                                                          

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with NTCA_SYNE7 | P29283 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
           NTCA_SYNE7     3 ANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS 222
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------cNMP_binding-2xhkB03 B:24-116                                                                -----------------------------HTH_Crp_2-2xhkB01 B:146-220                                                -- Pfam domains (1)
           Pfam domains (2) ---------------------cNMP_binding-2xhkB04 B:24-116                                                                -----------------------------HTH_Crp_2-2xhkB02 B:146-220                                                -- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhh..---.....eee...eeee.......eeeeeee.eeeeeeee...eeeeeeee..eeee..hhhhhh.......eeee...eeeeee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------CNMP_BINDING_3  PDB: B:22-128 UniProt: 22-128                                                              -------------HTH_CRP_2  PDB: B:142-215 UniProt: 142-215                                ------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: B:173-19-------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhk B   3 ANENSLLTMFRELG---LPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS 222
                                    12   |   |22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
                                        16  20                                                                                                                                                                                                          

   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 2XHK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XHK)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NTCA_SYNE7 | P29283)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        NTCA_SYNE7 | P292832xgx 2xko 2xkp

(-) Related Entries Specified in the PDB File

2xgx CRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR NTCA FROM SYNECHOCOCCUS ELONGATUS (MERCURY DERIVATIVE)
2xko CRYSTAL STRUCTURE OF THE COMPLEX OF NTCA WITH ITS TRANSCRIPTIONAL CO-ACTIVATOR PIPX
2xkp NTCA FROM SYNECHOCOCCUS ELONGATUS: ACTIVE AND INACTIVE