Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF NITROGEN REGULATORY PROTEIN IIA-NTR FROM NEISSERIA MENINGITIDIS
 
Authors :  J. Ren, S. Sainsbury, N. S. Berrow, D. Alderton, J. E. Nettleship, D. K. S N. J. Saunders, R. J. Owens, Oxford Protein Production Facility (
Date :  16 Jun 05  (Deposition) - 20 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Nitrogen Regulation, Structural Genomics, Oppf, Oxford Protein Production Facility, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Ren, S. Sainsbury, N. S. Berrow, D. Alderton, J. E. Nettleship, D. K. Stammers, N. J. Saunders, R. J. Owens
Crystal Structure Of Nitrogen Regulatory Protein Iiantr Fro Neisseria Meningitidis
Bmc Struct. Biol. V. 5 13 2005
PubMed-ID: 16092953  |  Reference-DOI: 10.1186/1472-6807-5-13

(-) Compounds

Molecule 1 - PTS SYSTEM, NITROGEN REGULATORY IIA PROTEIN
    ChainsA
    EC Number2.7.1.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST17
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePTSN
    Organism ScientificNEISSERIA MENINGITIDIS
    Organism Taxid122586
    StrainMC58

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2A0J)

(-) Sites  (0, 0)

(no "Site" information available for 2A0J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A0J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A0J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A0J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A0J)

(-) Exons   (0, 0)

(no "Exon" information available for 2A0J)

(-) 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:146
 aligned with Q9K082_NEIMB | Q9K082 from UniProtKB/TrEMBL  Length:149

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
         Q9K082_NEIMB     2 SLIGEILPLSHIVLDMEVGSKKRLFEEAGLLLERESSLSHADVFECLFAREKLGSTGLGQGVAIPHGRHAGVKQATGAFIRTREPVGFDAPDGKPVSLIFILLVPENATGEHLEVLSKLAGKFSQKSIRESLMTVSSAEEVRAILT 147
               SCOP domains d2a0ja_ A: automated matches                                                                                                                       SCOP domains
               CATH domains 2a0jA00 A:2-147 Mannitol-specific EII; Chain A                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.eeeee...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.........ee..eeee......eeeeeeeeeee.........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a0j A   2 SLIGEILPLSHIVLDMEVGSKKRLFEEAGLLLERESSLSHADVFECLFAREKLGSTGLGQGVAIPHGRHAGVKQATGAFIRTREPVGFDAPDGKPVSLIFILLVPENATGEHLEVLSKLAGKFSQKSIRESLMTVSSAEEVRAILT 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A0J)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9K082_NEIMB | Q9K082)
molecular function
    GO:0103111    D-glucosamine PTS permease activity    Catalysis of the reaction: a [PTS enzyme I]-Npi-phospho-L-histidine + D-glucosamine <=> D-glucosamine 6-phosphate + a [PTS enzyme I]-L-histidine
    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: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: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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2a0j)
 
  Sites
(no "Sites" information available for 2a0j)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2a0j)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2a0j
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9K082_NEIMB | Q9K082
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.69
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q9K082_NEIMB | Q9K082
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2A0J)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2A0J)