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(-) Description

Title :  X-RAY STRUCTURE OF A PUTATIVE PHOSPHOPROTEIN PHOSPHATASE FROM ARABIDOPSIS THALIANA GENE AT1G05000
 
Authors :  G. E. Wesenberg, D. W. Smith, G. N. Phillips Jr. , E. Bitto, C. A. Bingman S. T. M. Allard, Center For Eukaryotic Structural Genomics (Ces
Date :  14 Oct 04  (Deposition) - 26 Oct 04  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Structural Genomics, Protein Structure Initiative, Psi, Cesg, Center For Eukaryotic Structural Genomics, At1G05000, Phosphoprotein Phosphatase, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Aceti, E. Bitto, A. F. Yakunin, M. Proudfoot, C. A. Bingman, R. O. Frederick, H. K. Sreenath, F. C. Vojtik, R. L. Wrobel, B. G. Fox, J. L. Markley, G. N. Phillips Jr.
Structural And Functional Characterization Of A Novel Phosphatase From The Arabidopsis Thaliana Gene Locus At1G05000.
Proteins V. 73 241 2008
PubMed-ID: 18433060  |  Reference-DOI: 10.1002/PROT.22041

(-) Compounds

Molecule 1 - AT1G05000
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP-13
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT1G05000
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: PQE DERIVATIVE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 30)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE
2SO412Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:150 , LYS A:151 , ARG A:152 , LYS A:154 , HIS A:155 , ARG A:156BINDING SITE FOR RESIDUE SO4 A 203
2AC2SOFTWAREGLY A:118 , LYS A:151 , ARG A:152 , ARG A:156BINDING SITE FOR RESIDUE SO4 A 204
3AC3SOFTWARECYS B:150 , LYS B:151 , ARG B:152 , LYS B:154 , HIS B:155 , ARG B:156BINDING SITE FOR RESIDUE SO4 B 203
4AC4SOFTWAREGLY B:118 , LYS B:151 , ARG B:152 , ARG B:156BINDING SITE FOR RESIDUE SO4 B 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:144 -Pro A:145
2His B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.Y1500_ARATH148-158
 		  2A:148-158
B:148-158
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.Y1500_ARATH148-158
 		  2A:148-158
B:148-158
Biological Unit 2 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.Y1500_ARATH148-158
 		  6A:148-158
B:148-158

(-) Exons   (0, 0)

(no "Exon" information available for 1XRI)

(-) 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:151
 aligned with Y1500_ARATH | Q9ZVN4 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:151
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 
          Y1500_ARATH    52 HLIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPESNLQFLKSNGIRLFQFGIEGNKEPFVNIPDHKIRMALKVLLDEKNHPVLIHCKRGKHRTGCLVGCLRKLQKWCLTSIFDEYQRFAAAKARVSDQRFMEIFDVSS 202
               SCOP domains d1xria_ A: Putative phosphatase At1g05000                                                                                                               SCOP domains
               CATH domains 1xriA00 A:52-202 Protein tyrosine phosphatase superfamily                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..eeee...hhhhhhhhhhhh..eeee......hhhhhhhhhhhh.eeee......hhhhh..hhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------TYR_PHOSPHA-------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xri A  52 HLIPPLNFSmVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPESNLQFLKSNGIRLFQFGIEGNKEPFVNIPDHKIRmALKVLLDEKNHPVLIHCKRGKHRTGCLVGCLRKLQKWCLTSIFDEYQRFAAAKARVSDQRFmEIFDVSS 202
                                    61        71        81        91       101       111       121       131 |     141       151       161       171       181       191   |   201 
                                    61-MSE                                                                 133-MSE                                                       195-MSE   


Chain B from PDB  Type:PROTEIN  Length:151
 aligned with Y1500_ARATH | Q9ZVN4 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:151
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 
          Y1500_ARATH    52 HLIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPESNLQFLKSNGIRLFQFGIEGNKEPFVNIPDHKIRMALKVLLDEKNHPVLIHCKRGKHRTGCLVGCLRKLQKWCLTSIFDEYQRFAAAKARVSDQRFMEIFDVSS 202
               SCOP domains d1xrib_ B: Putative phosphatase At1g05000                                                                                                               SCOP domains
               CATH domains 1xriB00 B:52-202 Protein tyrosine phosphatase superfamily                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..eeee...hhhhhhhhhhhh..eeee......hhhhhhhhhhh..eeee......hhhhh..hhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------TYR_PHOSPHA-------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xri B  52 HLIPPLNFSmVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPESNLQFLKSNGIRLFQFGIEGNKEPFVNIPDHKIRmALKVLLDEKNHPVLIHCKRGKHRTGCLVGCLRKLQKWCLTSIFDEYQRFAAAKARVSDQRFmEIFDVSS 202
                                    61        71        81        91       101       111       121       131 |     141       151       161       171       181       191   |   201 
                                    61-MSE                                                                 133-MSE                                                       195-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  (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 1XRI)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Y1500_ARATH | Q9ZVN4)
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.
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.

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        Y1500_ARATH | Q9ZVN4: 2q47

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