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(-) Description

Title :  CRYSTAL STRUCTURE OF THE P- AND N-DOMAINS OF COPA, A COPPER-TRANSPORTING P-TYPE ATPASE, BOUND WITH AMPPCP-MG
 
Authors :  T. Tsuda, C. Toyoshima
Date :  31 Mar 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  P-Type Atpase, Atp-Binding, Cell Membrane, Copper Transport, Hydrolase, Ion Transport, Magnesium, Membrane, Metal-Binding, Nucleotide-Binding, Phosphoprotein, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Tsuda, C. Toyoshima
Nucleotide Recognition By Copa, A Cu+-Transporting P-Type Atpase.
Embo J. V. 28 1782 2009
PubMed-ID: 19478797  |  Reference-DOI: 10.1038/EMBOJ.2009.143

(-) Compounds

Molecule 1 - PROBABLE COPPER-EXPORTING P-TYPE ATPASE A
    ChainsA, B
    EC Number3.6.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBAD
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 387-673
    GeneCOPA, PACS, AF_0473
    Organism ScientificARCHAEOGLOBUS FULGIDUS
    Organism Taxid2234

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:424 , LYS A:425 , THR A:426 , GLU A:457 , HIS A:462 , ILE A:464 , GLY A:490 , GLU A:491 , GLY A:492 , VAL A:500 , GLY A:501 , ASN A:502 , VAL A:532 , THR A:572 , GLY A:573 , ASP A:574 , LYS A:600 , MG A:998 , HOH A:1001 , HOH A:1156 , HOH A:1173 , HOH A:1190 , HOH A:1196 , HOH A:1199BINDING SITE FOR RESIDUE ACP A 997
2AC2SOFTWAREASP A:424 , LYS A:600 , ACP A:997 , HOH A:1001 , HOH A:1002 , HOH A:1003BINDING SITE FOR RESIDUE MG A 998
3AC3SOFTWAREASP B:424 , LYS B:425 , THR B:426 , GLU B:457 , SER B:460 , HIS B:462 , ILE B:464 , GLY B:490 , GLU B:491 , VAL B:493 , VAL B:500 , GLY B:501 , ASN B:502 , THR B:572 , GLY B:573 , ASP B:574 , LYS B:600 , HOH B:1454 , HOH B:1471 , HOH B:1480 , HOH B:1483 , HOH B:1486 , HOH B:1504BINDING SITE FOR RESIDUE ACP B 997

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A1C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A1C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A1C)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATPASE_E1_E2PS00154 E1-E2 ATPases phosphorylation site.COPA_ARCFU424-430
 
  2A:424-430
B:424-430

(-) Exons   (0, 0)

(no "Exon" information available for 3A1C)

(-) 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:267
 aligned with COPA_ARCFU | O29777 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:267
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       
           COPA_ARCFU   400 AELGILIKNADALEVAEKVTAVIFDKTGTLTKGKPEVTDLVPLNGDERELLRLAAIAERRSEHPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELALEKLEREAKTAVIVARNGRVEGIIAVSDTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEVLPHQKSEEVKKLQAKEVVAFVGDGINDAPALAQADLGIAVGSGSDVAVESGDIVLIRDDLRDVVAAIQLSR 666
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhhhhhh.eeeee..........eeeeeee...hhhhhhhhhhhhh....hhhhhhhhhhhhhh.........eeee...eeee..eeeehhhhhhhh....hhhhhhhhhhhhhh..eeeeeee..eeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh..eee......hhhhhhhhhh....eeeee....hhhhhhhh.eeeee............eee....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------ATPASE_-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1c A 400 AELGILIKNADALEVAEKVTAVIFDKTGTLTKGKPEVTDLVPLNGDERELLRLAAIAERRSEHPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELALEKLEREAKTAVIVARNGRVEGIIAVSDTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEVLPHQKSEEVKKLQAKEVVAFVGDGINDAPALAQADLGIAVGSGSDVAVESGDIVLIRDDLRDVVAAIQLSR 666
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       

Chain B from PDB  Type:PROTEIN  Length:273
 aligned with COPA_ARCFU | O29777 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:273
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669   
           COPA_ARCFU   400 AELGILIKNADALEVAEKVTAVIFDKTGTLTKGKPEVTDLVPLNGDERELLRLAAIAERRSEHPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELALEKLEREAKTAVIVARNGRVEGIIAVSDTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEVLPHQKSEEVKKLQAKEVVAFVGDGINDAPALAQADLGIAVGSGSDVAVESGDIVLIRDDLRDVVAAIQLSRKTMSKI 672
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhhhhhh.eeeeehhhhh.....eeeeeee...hhhhhhhhhhhhhh...hhhhhhhhhhhhhh..........eee...eeee..eeeehhhhhhhh....hhhhhhhhhhhhh...eeeeeee..eeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh..eee......hhhhhhhhhh....eeeee....hhhhhhhh.eeeee............eee....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------ATPASE_-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1c B 400 AELGILIKNADALEVAEKVTAVIFDKTGTLTKGKPEVTDLVPLNGDERELLRLAAIAERRSEHPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELALEKLEREAKTAVIVARNGRVEGIIAVSDTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEVLPHQKSEEVKKLQAKEVVAFVGDGINDAPALAQADLGIAVGSGSDVAVESGDIVLIRDDLRDVVAAIQLSRKTMSKI 672
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669   

   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 3A1C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A1C)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (COPA_ARCFU | O29777)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019829    cation-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 + cation(out) = ADP + phosphate + cation(in).
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0098655    cation transmembrane transport    A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006825    copper ion transport    The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0030001    metal ion transport    The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        COPA_ARCFU | O297772b8e 2hc8 2voy 3a1d 3a1e 3fry 3j08 3j09

(-) Related Entries Specified in the PDB File

2arf NMR STRUCTURE OF THE N-DOMAIN OF ATP7B
2b8e NUCLEOTIDE UNBOUND FORM
2iye SO4 BOUND FORM
3a1d ADP-MG BOUND FORM
3a1e HIS462GLN MUTANT