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(-) Description

Title :  STRUCTURE OF YGR203W, A YEAST PROTEIN TYROSINE PHOSPHATASE OF THE RHODANESE FAMILY
 
Authors :  A. U. Singer, X. Xu, H. Cui, J. Osipiuk, A. Joachimiak, A. M. Edwards, A. F. Yakunin, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)
Date :  31 Oct 08  (Deposition) - 25 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Phosphatase, Rhodanese-Like Family, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Proudfoot, G. Brown, A. U. Singer, X. Xu, H. Cui, A. M. Edwards, A. Joachimiak, A. Savchenko, A. F. Yakunin
Structure Of Ygr203W, A Yeast Protein Tyrosine Phosphatase Of The Rhodanese Family
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YGR203W
    Chains: A, B
    EC Number: 3.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: G7731, YGR203W
    Organism Common: BREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NH41Ligand/IonAMMONIUM ION
4SO48Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:81 , CYS A:90 , MSE A:91 , LEU A:92 , SER A:93 , GLN A:94 , GLN A:95 , ARG A:96 , HOH A:202BINDING SITE FOR RESIDUE SO4 A 149
02AC2SOFTWAREGLY A:40 , SER A:41 , ARG A:96 , HOH A:159 , HOH A:310BINDING SITE FOR RESIDUE SO4 A 150
03AC3SOFTWAREARG A:117 , ARG B:117BINDING SITE FOR RESIDUE SO4 A 151
04AC4SOFTWAREARG A:19 , TRP A:20 , THR A:26 , THR A:27 , THR A:28 , HOH A:282 , HOH A:300BINDING SITE FOR RESIDUE SO4 A 152
05AC5SOFTWAREARG A:72BINDING SITE FOR RESIDUE CL A 153
06AC6SOFTWARETRP B:52 , HIS B:53 , TYR B:54 , ARG B:72 , HOH B:223 , HOH B:227 , HOH B:309 , HOH B:311BINDING SITE FOR RESIDUE SO4 B 149
07AC7SOFTWAREGLY B:40 , SER B:41 , ARG B:96 , HOH B:256 , HOH B:278 , HOH B:322BINDING SITE FOR RESIDUE SO4 B 150
08AC8SOFTWAREARG B:81 , CYS B:90 , MSE B:91 , LEU B:92 , SER B:93 , GLN B:94 , GLN B:95 , ARG B:96 , HOH B:255BINDING SITE FOR RESIDUE SO4 B 151
09AC9SOFTWAREHIS B:47 , ILE B:48 , LYS B:49 , ASP B:50 , ALA B:140 , HOH B:214BINDING SITE FOR RESIDUE SO4 B 152
10BC1SOFTWAREASP A:145 , MSE B:102 , ARG B:106BINDING SITE FOR RESIDUE NH4 B 153

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F4A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F4A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F4A)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHODANESE_3PS50206 Rhodanese domain profile.YCH1_YEAST29-137
 		  2A:29-137
B:29-137

(-) Exons   (0, 0)

(no "Exon" information available for 3F4A)

(-) 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:144
 aligned with YCH1_YEAST | P42937 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144    
           YCH1_YEAST     5 SITNVKYLDPTELHRWMQEGHTTTLREPFQVVDVRGSDYMGGHIKDGWHYAYSRLKQDPEYLRELKHRLLEKQADGRGALNVIFHCMLSQQRGPSAAMLLLRSLDTAELSRCRLWVLRGGFSRWQSVYGDDESVTAGYLPDLWR 148
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3f4aA00 A:5-148 Oxidized Rhodanese, domain 1                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhh........eeeee.........ee...ee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhh.hhhhhh.eeeeee.hhhhhhhhhhh.....ee..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------RHODANESE_3  PDB: A:29-137 UniProt: 29-137                                                                   ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f4a A   5 SITNVKYLDPTELHRWmQEGHTTTLREPFQVVDVRGSDYmGGHIKDGWHYAYSRLKQDPEYLRELKHRLLEKQADGRGALNVIFHCmLSQQRGPSAAmLLLRSLDTAELSRCRLWVLRGGFSRWQSVYGDDESVTAGYLPDLWR 148
                                    14      | 24        34        44        54        64        74        84      | 94       104       114       124       134       144    
                                           21-MSE                 44-MSE                                         91-MSE    102-MSE                                          


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with YCH1_YEAST | P42937 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144    
           YCH1_YEAST     5 SITNVKYLDPTELHRWMQEGHTTTLREPFQVVDVRGSDYMGGHIKDGWHYAYSRLKQDPEYLRELKHRLLEKQADGRGALNVIFHCMLSQQRGPSAAMLLLRSLDTAELSRCRLWVLRGGFSRWQSVYGDDESVTAGYLPDLWR 148
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3f4aB00 B:5-148 Oxidized Rhodanese, domain 1                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhh........eeeee..hhhhh..ee...ee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhhhhh.....ee..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------RHODANESE_3  PDB: B:29-137 UniProt: 29-137                                                                   ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f4a B   5 SITNVKYLDPTELHRWmQEGHTTTLREPFQVVDVRGSDYmGGHIKDGWHYAYSRLKQDPEYLRELKHRLLEKQADGRGALNVIFHCmLSQQRGPSAAmLLLRSLDTAELSRCRLWVLRGGFSRWQSVYGDDESVTAGYLPDLWR 148
                                    14      | 24        34        44        54        64        74        84      | 94       104       114       124       134       144    
                                           21-MSE                 44-MSE                                         91-MSE    102-MSE
   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 3F4A)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F4A)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YCH1_YEAST | P42937)
molecular function
    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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    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.
    GO:0004792    thiosulfate sulfurtransferase activity    Catalysis of the reaction: hydrogen cyanide + thiosulfate = H(+) + sulfite + thiocyanate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    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.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        YCH1_YEAST | P42937: 3fs5

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