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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ONE DOMAIN OF THE PTS SYSTEM, IIABC COMPONENT FROM CLOSTRIDIUM DIFFICILE
 
Authors :  R. Zhang, L. Bigelow, G. Cobb, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  17 Aug 09  (Deposition) - 20 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pts System, Iiabc Component, Psi, Structural Genomics, Mcsg, Protein Structure Initiative, Midwest Center For Structural Genomics, Cell Membrane, Kinase, Membrane, Phosphotransferase System, Sugar Transport, Transferase, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Zhang, L. Bigelow, G. Cobb, A. Joachimiak
The Crystal Structure Of One Domain Of The Pts System, Iiab Component From Clostridium Difficile
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PTS SYSTEM, IIABC COMPONENT
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG19
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 2-93
    Organism ScientificCLOSTRIDIUM DIFFICILE
    Organism Taxid272563
    Strain630

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:28 , HOH A:149 , HOH A:156 , GLU B:40 , GLU B:91BINDING SITE FOR RESIDUE ZN B 96
2AC2SOFTWAREGLU A:40 , GLU A:91 , HOH A:163 , CYS B:28 , HOH B:165BINDING SITE FOR RESIDUE ZN B 97

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IPJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3IPJ)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:95
 aligned with Q188R0_PEPD6 | Q188R0 from UniProtKB/TrEMBL  Length:624

    Alignment length:95
                              1                                                                                            
                              |      8        18        28        38        48        58        68        78        88     
          Q188R0_PEPD6    - --MNKYNKIANELIKIIGEDNIISITHCATRLRVMVKDREIINDKKVEKVDEVKGVFFTSGQYQIILGTGIVNKVYAEVEKMGLKTLSKKEQDEL 93
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...eeeeee...eeeeee.hhhhhhhhhhhh.....eeeee..eeeee...hhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                  3ipj A  1 SNANKYNKIANELIKIIGEDNIISITHCATRLRVMVKDREIINDKKVEKVDEVKGVFFTSGQYQIILGTGIVNKVYAEVEKMGLKTLSKKEQDEL 95
                                    10        20        30        40        50        60        70        80        90     

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with Q188R0_PEPD6 | Q188R0 from UniProtKB/TrEMBL  Length:624

    Alignment length:95
                              1                                                                                            
                              |      8        18        28        38        48        58        68        78        88     
          Q188R0_PEPD6    - --MNKYNKIANELIKIIGEDNIISITHCATRLRVMVKDREIINDKKVEKVDEVKGVFFTSGQYQIILGTGIVNKVYAEVEKMGLKTLSKKEQDEL 93
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...eeeeee...eeeeee.hhhhhhhhhhh......eeeee..eeeee...hhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                  3ipj B  1 SNANKYNKIANELIKIIGEDNIISITHCATRLRVMVKDREIINDKKVEKVDEVKGVFFTSGQYQIILGTGIVNKVYAEVEKMGLKTLSKKEQDEL 95
                                    10        20        30        40        50        60        70        80        90     

   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  (0, 0)

(no "SCOP Domain" information available for 3IPJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IPJ)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q188R0_PEPD6 | Q188R0)
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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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.
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:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    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: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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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