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(-) Description

Title :  CONFORMATIONAL CHANGES IN THE CATALYTIC DOMAIN OF THE CPX-ATPASE COPB-B UPON NUCLEOTIDE BINDING
 
Authors :  C. Voellmecke, C. Schlicker, M. Luebben, E. Hofmann
Date :  18 May 11  (Deposition) - 30 May 12  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, P-Type Atpase, Copb, Heavy Metal Translocation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Voellmecke, C. Schlicker, M. Luebben, E. Hofmann
Conformational Changes In The Catalytic Domain Of The Cpx-Atpase Copb-B Upon Nucleotide Binding
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COPPER-TRANSPORTING ATPASE
    Chains: A, B
    EC Number: 3.6.1.36, 3.6.3.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET27
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 383-645
    Mutation: YES
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 273057
    Strain: P2

 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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1A991Ligand/Ion5'-O-[(S)-HYDROXY{[(R)-HYDROXY({(S)-HYDROXY[(1S)-1-(2-NITROPHENYL)ETHOXY]PHOSPHORYL}OXY)PHOSPHORYL]OXY}PHOSPHORYL]ADENOSINE
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1A991Ligand/Ion5'-O-[(S)-HYDROXY{[(R)-HYDROXY({(S)-HYDROXY[(1S)-1-(2-NITROPHENYL)ETHOXY]PHOSPHORYL}OXY)PHOSPHORYL]OXY}PHOSPHORYL]ADENOSINE
2ATP-1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1A99-1Ligand/Ion5'-O-[(S)-HYDROXY{[(R)-HYDROXY({(S)-HYDROXY[(1S)-1-(2-NITROPHENYL)ETHOXY]PHOSPHORYL}OXY)PHOSPHORYL]OXY}PHOSPHORYL]ADENOSINE
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:424 , PRO A:426 , GLU A:445 , HIS A:450 , GLY A:478 , ILE A:479 , GLY A:480 , LYS A:494 , ILE A:501 , ASP A:517BINDING SITE FOR RESIDUE A99 A1636
2AC2SOFTWAREASN B:416 , THR B:418 , GLU B:445 , HIS B:450 , GLY B:478 , ILE B:479 , LYS B:494 , ILE B:501 , GLY B:542 , ASP B:543 , LYS B:569 , ASP B:588 , ASN B:591 , HOH B:2005 , HOH B:2006 , HOH B:2010 , HOH B:2022BINDING SITE FOR RESIDUE ATP B1636

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YJ5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile B:611 -Ser B:612

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YJ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YJ5)

(-) Exons   (0, 0)

(no "Exon" information available for 2YJ5)

(-) 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:246
 aligned with Q97UU7_SULSO | Q97UU7 from UniProtKB/TrEMBL  Length:695

    Alignment length:251
                                   394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634 
         Q97UU7_SULSO   385 LSLYEKMLHKGMIIKNSNVYEKIKEIDTIIFDKTGTLTYGTPIVTQFIGDSLSLAYAASVEALSSHPIAKAIVKYAKEQGVKILEVKDFKEISGIGVRGKISDKIIEVKKAENNNDIAVYINGEPIASFNISDVPRPNLKDYLEKLKNEGLKIIILSGDKEDKVKELSKELNIQEYYSNLSPEDKVRIIEKLKQNGNKVLMIGDGVNDAAALALADVSVAMGNGVDISKNVADIILVSNDIGTLLGLIKNR 635
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.eee...hhhhhhh...eeeeehhhhh.....eeeeee.hhhhhhhhhhhhh...hhhhhhhhhhhhhh.......eeeeee...eeeeee..eeeeeee......eeeee..eeeeeeeee......hhhhhhhhhhhhheeeee...hhhhhhhhhhhh....ee...hhhhhhhhhhhhhh....eeeee....hhhhhh...eeeee..-----.....eee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yj5 A 385 LSLYEKMLHKGMIIKNSNVYEKIKEIDTIIFNKTGTLTYGTPIVTQFIGDSLSLAYAASVEALSSHPIAKAIVKYAKEQGVKILEVKDFKEISGIGVRGKISDKIIEVKKAENNNDIAVYINGEPIASFNISDVPRPNLKDYLEKLKNEGLKIIILSGDKEDKVKELSKELNIQEYYSNLSPEDKVRIIEKLKQNGNKVLMIGDGVNDAAALALADVSVAMGN-----KNVADIILVSNDIGTLLGLIKNR 635
                                   394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604  |    614       624       634 
                                                                                                                                                                                                                                                        607   613                      


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with Q97UU7_SULSO | Q97UU7 from UniProtKB/TrEMBL  Length:695

    Alignment length:252
                                   393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633  
         Q97UU7_SULSO   384 ALSLYEKMLHKGMIIKNSNVYEKIKEIDTIIFDKTGTLTYGTPIVTQFIGDSLSLAYAASVEALSSHPIAKAIVKYAKEQGVKILEVKDFKEISGIGVRGKISDKIIEVKKAENNNDIAVYINGEPIASFNISDVPRPNLKDYLEKLKNEGLKIIILSGDKEDKVKELSKELNIQEYYSNLSPEDKVRIIEKLKQNGNKVLMIGDGVNDAAALALADVSVAMGNGVDISKNVADIILVSNDIGTLLGLIKNR 635
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.eee..hhhhhhhhhh.eeeee..........eeeeee.hhhhhhhhhhhhh...hhhhhhhhhhhhhh.......eeeeee...eeeeee..eeeeeee......eeeee..eeeeeeeee......hhhhhhhhhhhhheeeee...hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhh....eeeee....hhhhhhhh.eeeee.hhhhhh.....eee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yj5 B 384 ALSLYEKMLHKGMIIKNSNVYEKIKEIDTIIFNKTGTLTYGTPIVTQFIGDSLSLAYAASVEALSSHPIAKAIVKYAKEQGVKILEVKDFKEISGIGVRGKISDKIIEVKKAENNNDIAVYINGEPIASFNISDVPRPNLKDYLEKLKNEGLKIIILSGDKEDKVKELSKELNIQEYYSNLSPEDKVRIIEKLKQNGNKVLMIGDGVNDAAALALADVSVAMGNGVDISKNVADIILVSNDIGTLLGLIKNR 635
                                   393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633
   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 2YJ5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YJ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YJ5)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q97UU7_SULSO | Q97UU7)
molecular function
    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:0043682    copper-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 + Cu2+ = ADP + phosphate + Cu2+, directly driving the transport of the copper ions across a membrane.
    GO:0008900    hydrogen:potassium-exchanging 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 + H+(in) + K+(out) = ADP + phosphate + H+(out) + K+(in).
    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:0035434    copper ion transmembrane transport    The directed movement of copper cation across a membrane.
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    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.
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:0005887    integral component of plasma membrane    The component of the plasma 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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/TrEMBL
        Q97UU7_SULSO | Q97UU7: 2iye 2yj3 2yj4 2yj6

(-) Related Entries Specified in the PDB File

2iye STRUCTURE OF CATALYTIC CPX-ATPASE DOMAIN COPB-B
2yj3 CONFORMATIONAL CHANGES IN THE CATALYTIC DOMAIN OF THE CPX-ATPASE COPB-B UPON NUCLEOTIDE BINDING
2yj4 CONFORMATIONAL CHANGES IN THE CATALYTIC DOMAIN OF THE CPX-ATPASE COPB-B UPON NUCLEOTIDE BINDING
2yj6 CONFORMATIONAL CHANGES IN THE CATALYTIC DOMAIN OF THE CPX-ATPASE COPB-B UPON NUCLEOTIDE BINDING