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(-) Description

Title :  CRYSTAL STRUCTURE OF CIONA INTESTINALIS VOLTAGE SENSOR-CONTAINING PHOSPHATASE (CI-VSP), RESIDUES 241-576(C363S), COMPLEXED WITH D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
 
Authors :  L. Liu, S. C. Kohout, Q. Xu, S. Muller, C. Kimberlin, E. Y. Isacoff, D. L. M
Date :  08 Dec 11  (Deposition) - 09 May 12  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ptp, C2, Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Liu, S. C. Kohout, Q. Xu, S. Muller, C. R. Kimberlin, E. Y. Isacoff, D. L. Minor
A Glutamate Switch Controls Voltage-Sensitive Phosphatase Function.
Nat. Struct. Mol. Biol. V. 19 633 2012
PubMed-ID: 22562138  |  Reference-DOI: 10.1038/NSMB.2289

(-) Compounds

Molecule 1 - VOLTAGE-SENSOR CONTAINING PHOSPHATASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: ROSETTA DE3 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 241-576
    Gene: CI-VSP
    Mutation: YES
    Organism Common: TRANSPARENT SEA SQUIRT
    Organism Scientific: CIONA INTESTINALIS
    Organism Taxid: 7719

 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, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1I3P4Ligand/IonD-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1I3P2Ligand/IonD-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1I3P2Ligand/IonD-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:72 , HOH A:96 , HOH A:107 , HOH A:129 , HOH A:175 , ASP A:331 , HIS A:332 , SER A:363 , LYS A:364 , GLY A:365 , GLY A:366 , LYS A:367 , GLY A:368 , ARG A:369 , THR A:370 , THR A:412 , TYR A:522 , HOH A:586 , HOH A:605 , HOH A:649 , HOH A:665 , HOH A:682 , HOH A:687 , HOH A:697 , HOH A:705BINDING SITE FOR RESIDUE I3P A 1
2AC2SOFTWAREHOH A:108 , ARG A:281 , ARG A:286 , ARG A:313 , LYS A:364 , HOH A:664BINDING SITE FOR RESIDUE I3P A 2
3AC3SOFTWAREHOH B:13 , HOH B:80 , HOH B:126 , HOH B:150 , ASP B:331 , HIS B:332 , SER B:363 , LYS B:364 , GLY B:365 , GLY B:366 , LYS B:367 , GLY B:368 , ARG B:369 , THR B:370 , THR B:412 , TYR B:522 , HOH B:584 , HOH B:599 , HOH B:610 , HOH B:613 , HOH B:621 , HOH B:743BINDING SITE FOR RESIDUE I3P B 3
4AC4SOFTWAREHOH B:112 , ARG B:286 , ARG B:313 , LYS B:364BINDING SITE FOR RESIDUE I3P B 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V0H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:282 -Ser A:283
2Ser B:279 -Gly B:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V0H)

(-) Exons   (0, 0)

(no "Exon" information available for 3V0H)

(-) 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:326
 aligned with Q4W8A1_CIOIN | Q4W8A1 from UniProtKB/TrEMBL  Length:576

    Alignment length:326
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569      
         Q4W8A1_CIOIN   250 QNKRRYRKDGFDLDLTYVTDHVIAMSFPSSGRQSLFRNPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHCKGGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRTDFEVGDVFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFSDAED 575
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee..eeee.............hhhhhhhhhhhhh...eeeeeee.....hhhhhh..eeeeee......hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.........eeeeeeeee............eeeeeee..eeeeeee......eeeeee....eeeeee........eeeeeeee.......hhhhh.eeeeee.hhh...eeeee.hhh....hhhhh.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v0h A 250 QNKRRYRKDGFDLDLTYVTDHVIAMSFPSSGRQSLFRNPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHSKGGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRTDFEVGDVFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFSDAED 575
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569      


Chain B from PDB  Type:PROTEIN  Length:327
 aligned with Q4W8A1_CIOIN | Q4W8A1 from UniProtKB/TrEMBL  Length:576

    Alignment length:327
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       
         Q4W8A1_CIOIN   249 SQNKRRYRKDGFDLDLTYVTDHVIAMSFPSSGRQSLFRNPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHCKGGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRTDFEVGDVFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFSDAED 575
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee.eeeee..eeee..ee........eehhhhhhhhhhhh...eeeeeee.....hhhhhh..eeeeee......hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh........eeeeeeeee............eeeeeee..eeeeeee......eeeeee....eeeeee........eeeeeeee.......hhhhh.eeeeee.hhh...eeeee.hhh....hhhhh.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v0h B 249 SQNKRRYRKDGFDLDLTYVTDHVIAMSFPSSGRQSLFRNPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHSKGGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRTDFEVGDVFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFSDAED 575
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568
   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 3V0H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V0H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V0H)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q4W8A1_CIOIN | Q4W8A1)
molecular function
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0008138    protein tyrosine/serine/threonine phosphatase activity    Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0005244    voltage-gated ion channel activity    Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other 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:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q4W8A1_CIOIN | Q4W8A1: 4g7v 4g80
UniProtKB/TrEMBL
        Q4W8A1_CIOIN | Q4W8A1: 3awe 3awf 3awg 3v0d 3v0e 3v0f 3v0g 3v0i 3v0j 4g7y

(-) Related Entries Specified in the PDB File

3v0d COMPLEX WITH LIPID HEAD GROUP
3v0e
3v0f
3v0g
3v0i
3v0j