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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF THE ABC TRANSPORTER, ATP-BINDING PROTEIN FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  Y. Kim, M. Zhou, L. Freeman, A. Joachimiak, Midwest Center For Struc Genomics (Mcsg)
Date :  28 Jul 07  (Deposition) - 14 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Amino-Acid Transport, Atp-Binding, Hydrolase, Inner Membrane, Membrane, Nucleotide-Binding, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kim, M. Zhou, L. Freeman, A. Joachimiak
The Soluble Domain Of The Abc Transporter, Atp-Binding Protein From Vibrio Parahaemolyticus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHIONINE IMPORT ATP-BINDING PROTEIN METN
    ChainsA, B
    EC Number3.6.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPMCSG7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 247-344
    GeneMETN, VP0706
    Organism ScientificVIBRIO PARAHAEMOLYTICUS
    Organism Taxid223926
    StrainRIMD 2210633

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2QRR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QRR)

(-) 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:97
 aligned with METN_VIBPA | Q87RS1 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:97
                                   257       267       277       287       297       307       317       327       337       
           METN_VIBPA   248 SIPEDYQARLQPNRVEGSYPLVRMEFTGATVDAPLMSQISRKYNIDVSILSSDLDYAGGVKFGMMVAELFGNEQDDSAAIEYLREHNVKVEVLGYVL 344
               SCOP domains d2qrra1 A:2-98 Methionine import ATP-binding protein MetN                                         SCOP domains
               CATH domains 2qrrA00 A:2-98  [code=3.30.70.260, no name defined]                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhee.......eeeeeeee.......hhhhhhhhhh..eeeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 2qrr A   2 SIPEDYQARLQPNRVEGSYPLVRmEFTGATVDAPLmSQISRKYNIDVSILSSDLDYAGGVKFGmmVAELFGNEQDDSAAIEYLRENNVKVEVLGYVL  98
                                    11        21   |    31     |  41        51        61   ||   71        81        91       
                                                  25-MSE      37-MSE                      65-MSE                             
                                                                                           66-MSE                            

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with METN_VIBPA | Q87RS1 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:98
                                   256       266       276       286       296       306       316       326       336        
           METN_VIBPA   247 LSIPEDYQARLQPNRVEGSYPLVRMEFTGATVDAPLMSQISRKYNIDVSILSSDLDYAGGVKFGMMVAELFGNEQDDSAAIEYLREHNVKVEVLGYVL 344
               SCOP domains d2qrrb_ B: Methionine import ATP-binding protein MetN                                              SCOP domains
               CATH domains 2qrrB00 B:1-98  [code=3.30.70.260, no name defined]                                                CATH domains
           Pfam domains (1) ------------------NIL-2qrrB01 B:19-94                                                         ---- Pfam domains (1)
           Pfam domains (2) ------------------NIL-2qrrB02 B:19-94                                                         ---- Pfam domains (2)
         Sec.struct. author ...hhhhhhhee.......eeeeeeee.......hhhhhhhhhh..eeeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2qrr B   1 LSIPEDYQARLQPNRVEGSYPLVRmEFTGATVDAPLmSQISRKYNIDVSILSSDLDYAGGVKFGmmVAELFGNEQDDSAAIEYLRENNVKVEVLGYVL  98
                                    10        20    |   30      | 40        50        60    ||  70        80        90        
                                                   25-MSE      37-MSE                      65-MSE                             
                                                                                            66-MSE                            

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (METN_VIBPA | Q87RS1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042626    ATPase activity, coupled to transmembrane movement of substances    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
    GO:0048474    D-methionine transmembrane transporter activity    Enables the transfer of D-methionine from one side of a membrane to the other.
    GO:0015424    amino acid-transporting ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + amino acid(out/in) = ADP + phosphate + amino acid(in/out).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0048473    D-methionine transport    The directed movement of D-methionine into, out of, within, or between cells.
    GO:0003333    amino acid transmembrane transport    The directed movement of amino acids, organic acids containing one or more amino substituents across a membrane by means of some agent such as a transporter or pore.
    GO:0006865    amino acid transport    The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0015821    methionine transport    The directed movement of methionine, 2-amino-4-(methylthio)butanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
    GO:0009276    Gram-negative-bacterium-type cell wall    The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
    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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