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(-) Description

Title :  CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE ACTIVATOR ADENINE
 
Authors :  S. Wang, C. V. Stauffacher, R. L. Van Etten
Date :  22 Sep 99  (Deposition) - 01 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Alpha-Beta, Tyrosine Phosphatase, Ltp1, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Wang, C. V. Stauffacher, R. L. Van Etten
Structural And Mechanistic Basis For The Activation Of A Low-Molecular Weight Protein Tyrosine Phosphatase By Adenine.
Biochemistry V. 39 1234 2000
PubMed-ID: 10684601  |  Reference-DOI: 10.1021/BI991515+
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSINE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: INACTIVE MUTANT OF LTP1 THAT THE NUCLEOPHILE CYSTEINE IS MUTATED TO ALANINE IS USED.

 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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
2CL1Ligand/IonCHLORIDE ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADE-1Ligand/IonADENINE
2CL-1Ligand/IonCHLORIDE ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
2CL-1Ligand/IonCHLORIDE ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:13 , LEU A:14 , GLY A:15 , ASN A:16 , PHE A:17 , CYS A:18 , ARG A:19 , SER A:20 , HOH A:536BINDING SITE FOR RESIDUE PO4 A 402
2AC2SOFTWAREALA B:13 , LEU B:14 , GLY B:15 , ASN B:16 , PHE B:17 , CYS B:18 , ARG B:19 , SER B:20 , HOH B:458BINDING SITE FOR RESIDUE PO4 B 403
3AC3SOFTWARETHR A:48 , ASN A:97 , ASN A:100BINDING SITE FOR RESIDUE CL A 404
4AC4SOFTWARETYR B:51 , HIS B:52 , ASP B:132 , TRP B:134 , HOH B:410 , HOH B:458 , HOH B:485 , HOH B:518BINDING SITE FOR RESIDUE ADE B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D2A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D2A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D2A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D2A)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR073C1YPR073C.1XVI:692415-691930486PPAL_YEAST1-1611612A:5-160
B:5-160		156
156

(-) 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:156
 aligned with PPAL_YEAST | P40347 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:156
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155      
           PPAL_YEAST     6 PKISVAFICLGNFCRSPMAEAIFKHEVEKANLENRFNKIDSFGTSNYHVGESPDHRTVSICKQHGVKINHKGKQIKTKHFDEYDYIIGMDESNINNLKKIQPEGSKAKVCLFGDWNTNDGTVQTIIEDPWYGDIQDFEYNFKQITYFSKQFLKKEL 161
               SCOP domains d1d2aa_ A: Tyrosine phosphatase                                                                                                                              SCOP domains
               CATH domains 1d2aA00 A:5-160  [code=3.40.50.270, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhh.....eeeeeeee..........hhhhhhhhhhh.............hhhhhh.eeee.hhhhhhhhhhhh......eeee.....................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-160 UniProt: 1-161 [INCOMPLETE]                                                                                                           Transcript 1
                 1d2a A   5 PKISVAFIALGNFCRSPMAEAIFKHEVEKANLENRFNKIDSFGTSNYHVGESPDHRTVSICKQHGVKINHKGKQIKTKHFDEYDYIIGMDESNINNLKKIQPEGSKAKVCLFGDWNTNDGTVQTIIEDPWYGDIQDFEYNFKQITYFSKQFLKKEL 160
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154      


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with PPAL_YEAST | P40347 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:156
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155      
           PPAL_YEAST     6 PKISVAFICLGNFCRSPMAEAIFKHEVEKANLENRFNKIDSFGTSNYHVGESPDHRTVSICKQHGVKINHKGKQIKTKHFDEYDYIIGMDESNINNLKKIQPEGSKAKVCLFGDWNTNDGTVQTIIEDPWYGDIQDFEYNFKQITYFSKQFLKKEL 161
               SCOP domains d1d2ab_ B: Tyrosine phosphatase                                                                                                                              SCOP domains
               CATH domains 1d2aB00 B:5-160  [code=3.40.50.270, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhh.....eeeeeeee..........hhhhhhhhhh............hhhhhhh..eeee.hhhhhhhhhhhh......eeee.....................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:5-160 UniProt: 1-161 [INCOMPLETE]                                                                                                           Transcript 1
                 1d2a B   5 PKISVAFIALGNFCRSPMAEAIFKHEVEKANLENRFNKIDSFGTSNYHVGESPDHRTVSICKQHGVKINHKGKQIKTKHFDEYDYIIGMDESNINNLKKIQPEGSKAKVCLFGDWNTNDGTVQTIIEDPWYGDIQDFEYNFKQITYFSKQFLKKEL 160
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D2A)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PPAL_YEAST | P40347)
molecular function
    GO:0003993    acid phosphatase activity    Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
    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:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPAL_YEAST | P40347: 1d1p 1d1q

(-) Related Entries Specified in the PDB File

1d1p STRUCTURE OF THE WILD-TYPE LTP1 COMPLEXED WITH HEPES
1d1q STRUCTURE OF LTP1-C13A MUTANT COMPLEXED WITH THE SUBSTRATE PNPP