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(-) Description

Title :  NITROGEN REGULATORY BACTERIAL PROTEIN IIA-NITROGEN
 
Authors :  D. Bordo, R. Van Montfort, T. Pijning, K. H. Kalk, J. Reizer, M. H. Saier B. W. Dijkstra
Date :  25 Feb 98  (Deposition) - 15 Jul 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Phosphotransferase System, Nitrogen Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Bordo, R. L. Van Monfort, T. Pijning, K. H. Kalk, J. Reizer, M. H. Saier Jr. , B. W. Dijkstra
The Three-Dimensional Structure Of The Nitrogen Regulatory Protein Iiantr From Escherichia Coli.
J. Mol. Biol. V. 279 245 1998
PubMed-ID: 9636714  |  Reference-DOI: 10.1006/JMBI.1998.1753

(-) Compounds

Molecule 1 - NITROGEN REGULATORY IIA PROTEIN
    Cellular LocationCYTOPLASM
    ChainsA, B
    EC Number2.7.1.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainK12/W3110
    SynonymIIA-NITROGEN, ENZYME IIA-NTR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:97 , ASN A:101 , ARG B:57 , HIS B:73 , BME B:803 , HOH B:820BINDING SITE FOR RESIDUE SO4 B 701
2AC2SOFTWARETHR A:56 , MET A:60 , LYS B:134BINDING SITE FOR RESIDUE BME A 802
3AC3SOFTWAREALA A:95 , ASN A:101 , PRO A:103 , SO4 B:701BINDING SITE FOR RESIDUE BME B 803
4PH1UNKNOWNHIS A:73BY COMPARISON WITH IIA ENZYMES, THIS IS THE PHOSPHORYLATION SITE.
5PH2UNKNOWNHIS B:73BY COMPARISON WITH IIA ENZYMES, THIS IS THE PHOSPHORYLATION SITE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A6J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A6J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A6J)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTS_EIIA_TYPE_2PS51094 PTS_EIIA type-2 domain profile.PTSN_ECOLI12-156
 
  2A:12-156
B:12-156
2PTS_EIIA_TYPE_2_HISPS00372 PTS EIIA domains phosphorylation site signature 2.PTSN_ECOLI58-74
 
  2A:58-74
B:58-74
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTS_EIIA_TYPE_2PS51094 PTS_EIIA type-2 domain profile.PTSN_ECOLI12-156
 
  4A:12-156
B:12-156
2PTS_EIIA_TYPE_2_HISPS00372 PTS EIIA domains phosphorylation site signature 2.PTSN_ECOLI58-74
 
  4A:58-74
B:58-74

(-) Exons   (0, 0)

(no "Exon" information available for 1A6J)

(-) 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:150
 aligned with PTSN_ECOLI | P69829 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:150
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157
           PTSN_ECOLI     8 LQLSSVLNRECTRSRVHCQSKKRALEIISELAAKQLSLPPQVVFEAILTREKMGSTGIGNGIAIPHGKLEEDTLRAVGVFVQLETPIAFDAIDNQPVDLLFALLVPADQTKTHLHTLSLVAKRLADKTICRRLRAAQSDEELYQIITDTE 157
               SCOP domains d1a6ja_ A: Nitrogen regulatory bacterial protein IIa-ntr                                                                                               SCOP domains
               CATH domains 1a6jA00 A:8-157 Mannitol-specific EII; Chain A                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhh...hhh.........hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..............eeee.hhh...eeeeee................eeeeeeeehhh..hhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----PTS_EIIA_TYPE_2  PDB: A:12-156 UniProt: 12-156                                                                                                   - PROSITE (1)
                PROSITE (2) --------------------------------------------------PTS_EIIA_TYPE_2_H----------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a6j A   8 LQLSSVLNRECTRSRVHCQSKKRALEIISELAAKQLSLPPQVVFEAILTREKMGSTGIGNGIAIPHGKLEEDTLRAVGVFVQLETPIAFDAIDNQPVDLLFALLVPADQTKTHLHTLSLVAKRLADKTICRRLRAAQSDEELYQIITDTE 157
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with PTSN_ECOLI | P69829 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           PTSN_ECOLI     1 MTNNDTTLQLSSVLNRECTRSRVHCQSKKRALEIISELAAKQLSLPPQVVFEAILTREKMGSTGIGNGIAIPHGKLEEDTLRAVGVFVQLETPIAFDAIDNQPVDLLFALLVPADQTKTHLHTLSLVAKRLADKTICRRLRAAQSDEELYQIITDTE 157
               SCOP domains d1a6jb_ B: Nitrogen regulatory bacterial protein IIa-ntr                                                                                                      SCOP domains
               CATH domains 1a6jB00 B:1-157 Mannitol-specific EII; Chain A                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..hhh.........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh............eeee.......eeeeee................eeeeeeeehhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------PTS_EIIA_TYPE_2  PDB: B:12-156 UniProt: 12-156                                                                                                   - PROSITE (1)
                PROSITE (2) ---------------------------------------------------------PTS_EIIA_TYPE_2_H----------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a6j B   1 MTNNDTTLQLSSVLNRECTRSRVHCQSKKRALEIISELAAKQLSLPPQVVFEAILTREKMGSTGIGNGIAIPHGKLEEDTLRAVGVFVQLETPIAFDAIDNQPVDLLFALLVPADQTKTHLHTLSLVAKRLADKTICRRLRAAQSDEELYQIITDTE 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A6J)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PTSN_ECOLI | P69829)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030295    protein kinase activator activity    Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0008982    protein-N(PI)-phosphohistidine-sugar phosphotransferase activity    Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0032147    activation of protein kinase activity    Any process that initiates the activity of an inactive protein kinase.
    GO:0034219    carbohydrate transmembrane transport    The process in which a carbohydrate is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0009401    phosphoenolpyruvate-dependent sugar phosphotransferase system    The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0032412    regulation of ion transmembrane transporter activity    Any process that modulates the activity of an ion transporter.
    GO:0010243    response to organonitrogen compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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