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(-) Description

Title :  STRUCTURE OF A PUTATIVE NUCLEOTIDE PHOSPHATASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  A. Dong, C. Yang, A. U. Singer, E. Evdokimova, M. Kudritsdka, G. Brown, A. M. Edwards, A. Joachimiak, A. Savchenko, A. F. Yakunin, Midwest Ce Structural Genomics (Mcsg)
Date :  07 Jul 10  (Deposition) - 18 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Suppresses The 6-Au Sensitivity Of Transcription Elongation Factor S- Ii, Resistance To Pyrimidine Derivatives, Structural Genomics, Psi- 2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Alpha-Beta Hydrolase, Pyrimidine Nucleotidase, Metal Dependent, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Brown, E. Evdokimova, M. Kudritska, A. Dong, C. Yang, A. U. Singer, A. M. Edwards, A. Savchenko, A. F. Yakunin
Structure Of A Putative Nucleotide Phosphatase From Saccharomyces Cerevisiae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE NUCLEOTIDE PHOSPHATASE
    Chains: A
    EC Number: 3.1.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P11
    Expression System Strain: BL21 DE3 GOLD MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SDT1, SSM1, YGL224C
    Organism Common: BREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: S288C
    Synonym: PROTEIN SSM1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3NA1Ligand/IonSODIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:164 , THR A:165 , THR A:189 , TYR A:190 , CYS A:191 , VAL A:200 , ALA A:207 , LYS A:210 , HOH A:331BINDING SITE FOR RESIDUE EDO A 281
2AC2SOFTWAREALA A:11 , GLN A:14 , ASN A:15 , VAL A:275 , VAL A:276 , SER A:277 , ASP A:278BINDING SITE FOR RESIDUE EDO A 282
3AC3SOFTWAREASP A:61 , ASP A:63 , ASP A:228 , HOH A:371 , HOH A:372 , HOH A:373BINDING SITE FOR RESIDUE NA A 283
4AC4SOFTWAREARG A:112 , GLY A:113 , LYS A:157BINDING SITE FOR RESIDUE CL A 285
5AC5SOFTWARELEU A:10 , GLN A:14 , ARG A:112 , ARG A:151 , PRO A:273 , SER A:277 , PHE A:280BINDING SITE FOR RESIDUE PEG A 286

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:202 -Pro A:203

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NUQ)

(-) 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:268
 aligned with SDT1_YEAST | P53078 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
           SDT1_YEAST     1 MTVEYTASDLATYQNEVNEQIAKNKAHLESLTHPGSKVTFPIDQDISATPQNPNLKVFFFDIDNCLYKSSTRIHDLMQQSILRFFQTHLKLSPEDAHVLNNSYYKEYGLAIRGLVMFHKVNALEYNRLVDDSLPLQDILKPDIPLRNMLLRLRQSGKIDKLWLFTNAYKNHAIRCLRLLGIADLFDGLTYCDYSRTDTLVCKPHVKAFEKAMKESGLARYENAYFIDDSGKNIETGIKLGMKTCIHLVENEVNEILGQTPEGAIVISDILELPHVVSDLF 280
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh..............--------....eeee.........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhh...hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.......eee..............hhhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh..eeeee.....----.......eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nuq A   1 MTVEYTASDLATYQNEVNEQIAKNKAHLESLTHPGSKVTFPIDQ--------PNLKVFFFDIDNCLYKSSTRIHDLMQQSILRFFQTHLKLSPEDAHVLNNSYYKEYGLAIRGLVMFHKVNALEYNRLVDDSLPLQDILKPDIPLRNMLLRLRQSGKIDKLWLFTNAYKNHAIRCLRLLGIADLFDGLTYCDYSRTDTLVCKPHVKAFEKAMKESGLARYENAYFIDDSGKNIETGIKLGMKTCIHLVENEV----GQTPEGAIVISDILELPHVVSDLF 280
                                    10        20        30        40   |     -  |     60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 |    |260       270       280
                                                                      44       53                                                                                                                                                                                                    252  257
   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 3NUQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SDT1_YEAST | P53078)
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:0008252    nucleotidase activity    Catalysis of the reaction: a nucleotide + H2O = a nucleoside + phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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    Lys A:202 - Pro A:203   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SDT1_YEAST | P53078: 3onn 3opx

(-) Related Entries Specified in the PDB File

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