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(-) Description

Title :  CRYSTAL STRUCTURE OF PTEN-LIKE DOMAIN OF CI-VSP G356A MUTANT (248-576)
 
Authors :  M. Matsuda, S. Sakata, K. Takeshita, M. Suzuki, E. Yamashita, Y. Okamur A. Nakagawa
Date :  19 Mar 11  (Deposition) - 04 May 11  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ptdins(3, 4, 5)P3, Phosphatase, Ion Channel, Hydrolase, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Matsuda, K. Takeshita, T. Kurokawa, S. Sakata, M. Suzuki, E. Yamashita, Y. Okamura, A. Nakagawa
Crystal Structure Of The Cytoplasmic Phosphatase And Tensin Homolog (Pten)-Like Region Of Ciona Intestinalis Voltage-Sensing Phosphatase Provides Insight Into Substrate Specificity And Redox Regulation Of The Phosphoinositide Phosphatase Activity
J. Biol. Chem. V. 286 23368 2011
PubMed-ID: 21543329  |  Reference-DOI: 10.1074/JBC.M110.214361

(-) Compounds

Molecule 1 - VOLTAGE-SENSOR CONTAINING PHOSPHATASE
    Chains: A, B, C
    EC Number: 3.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32
    Expression System Strain: BL21(DE3)CODONPLUS-RILP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PTEN-LIKE REGION, RESIDUES 248-576
    Mutation: YES
    Organism Common: TRANSPARENT SEA SQUIRT
    Organism Scientific: CIONA INTESTINALIS
    Organism Taxid: 7719
    Synonym: CI-VSP

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:165 , THR A:268 , ASP A:269 , HIS A:270 , LYS A:383BINDING SITE FOR RESIDUE SO4 A 3
02AC2SOFTWARECYS A:363 , LYS A:364 , ALA A:365 , GLY A:366 , LYS A:367 , GLY A:368 , ARG A:369 , THR A:370 , GLU A:411BINDING SITE FOR RESIDUE SO4 A 6
03AC3SOFTWAREARG A:454 , SER A:515 , LYS A:516 , SER A:517BINDING SITE FOR RESIDUE SO4 A 8
04AC4SOFTWAREHOH B:163 , THR B:268 , ASP B:269 , HIS B:270 , LYS B:383BINDING SITE FOR RESIDUE SO4 B 1
05AC5SOFTWAREHOH B:120 , HOH B:241 , CYS B:363 , LYS B:364 , ALA B:365 , LYS B:367 , GLY B:368 , ARG B:369 , THR B:370 , GLU B:411BINDING SITE FOR RESIDUE SO4 B 2
06AC6SOFTWAREARG B:454 , SER B:515 , LYS B:516 , ARG C:397BINDING SITE FOR RESIDUE SO4 C 4
07AC7SOFTWAREHOH C:174 , THR C:268 , ASP C:269 , HIS C:270 , LYS C:383BINDING SITE FOR RESIDUE SO4 C 5
08AC8SOFTWAREHOH C:15 , CYS C:363 , LYS C:364 , ALA C:365 , GLY C:366 , LYS C:367 , GLY C:368 , ARG C:369 , THR C:370 , GLU C:411BINDING SITE FOR RESIDUE SO4 C 7
09AC9SOFTWARELYS B:342 , ARG C:454 , SER C:515 , LYS C:516BINDING SITE FOR RESIDUE SO4 C 9
10BC1SOFTWAREHOH C:185 , CYS C:310 , SER C:311 , GLU C:312 , ARG C:313 , CYS C:363 , ARG C:369BINDING SITE FOR RESIDUE SO4 C 10

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:310 -A:363
2B:310 -B:363
3C:310 -C:363

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AWG)

(-) 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:306
 aligned with Q4W8A1_CIOIN | Q4W8A1 from UniProtKB/TrEMBL  Length:576

    Alignment length:318
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563        
         Q4W8A1_CIOIN   254 RYRKDGFDLDLTYVTDHVIAMSFPSSGRQSLFRNPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHCKGGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRTDFEVGDVFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFS 571
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeee..eeee.....-------.hhhhhhhhhhhhh...eeeeeee.....hhhhhh..eeeeee......hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhh.-----hhhhhh.hhhhhhhhhhhhhhhhhh..........eeeeeeee............eeeeeee..eeeeeee......eeeeeehhh.eeeeee........eeeeeeee.......hhhhh.eeeeee.hhh...eeeehhhhh....hhhhh.......eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3awg A 254 RYRKDGFDLDLTYVTDHVIAMSFPSS-------NPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHCKAGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRT-----DVFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFS 571
                                   263       273     |   -   |   293       303       313       323       333       343       353       363       373       383       393     |   - |     413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563        
                                                   279     287                                                                                                             399   405                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:306
 aligned with Q4W8A1_CIOIN | Q4W8A1 from UniProtKB/TrEMBL  Length:576

    Alignment length:319
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563         
         Q4W8A1_CIOIN   254 RYRKDGFDLDLTYVTDHVIAMSFPSSGRQSLFRNPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHCKGGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRTDFEVGDVFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFSD 572
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee.eeeee..eeee.....-------.hhhhhhhhhhhhh...eeeeeee.....hhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh------......hhhhhhhhhhhhhhhhhh..........eeeeeeee............eeeeeee...eeeeee......eeeeee....eeeeee........eeeeeeee.............eeeeee.hhh...eeeehhhhh....hhhhh.......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3awg B 254 RYRKDGFDLDLTYVTDHVIAMSFPSS-------NPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHCKAGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRT------VFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFSD 572
                                   263       273     |   -   |   293       303       313       323       333       343       353       363       373       383       393     |   -  |    413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563         
                                                   279     287                                                                                                             399    406                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:308
 aligned with Q4W8A1_CIOIN | Q4W8A1 from UniProtKB/TrEMBL  Length:576

    Alignment length:319
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563         
         Q4W8A1_CIOIN   254 RYRKDGFDLDLTYVTDHVIAMSFPSSGRQSLFRNPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHCKGGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRTDFEVGDVFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFSD 572
               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..........eeeeeeee............eeeeeee..eeeeeee......eeeeee....eeeeee........eeeeeeee.......hhhhh.eeeeee.hhh...eeeehhhhh....hhhhh.......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3awg C 254 RYRKDGFDLDLTYVTDHVIAMSFPSS-------NPIGEVSRFFKTKHPDKFRIYNLCSERGYDETKFDNHVYRVMIDDHNVPTLVDLLKFIDDAKVWMTSDPDHVIAIHCKAGKGRTGTLVSSWLLEDGKFDTAKEALEYFGSRRT----GDVFQGVETASQIRYVGYFEKIKKNYGGQLPPMKKLKVTGVTITAIQGVGRGNGSDLSMQIVSERQEVLLCKFAEGYNCALQYDATDDCVTCEVKNCPVLAGDIKVRFMSTSKSLPRGYDNCPFYFWFNTSLVEGDHVTLKREEIDNPHKKKTWKIYRDNFTVKLTFSD 572
                                   263       273     |   -   |   293       303       313       323       333       343       353       363       373       383       393     |   -|      413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563         
                                                   279     287                                                                                                             399  404
   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 3AWG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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 3v0d 3v0e 3v0f 3v0g 3v0h 3v0i 3v0j 4g7y

(-) Related Entries Specified in the PDB File

3awe 3awf