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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRIMIDINE 5 -NUCLEOTIDASE SDT1 FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH URIDINE 5'-MONOPHOSPHATE
 
Authors :  M. K. Teng, L. W. Niu, N. Shi
Date :  02 Sep 10  (Deposition) - 02 Mar 11  (Release) - 02 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Nucleotidase, U5P Binding, Magnesium Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Shi, M. K. Teng, L. W. Niu
Crystal Structure Of Pyrimidine 5 -Nucleotidase Sdt1 From Saccharomyces Cerevisiae Complexed With Uridine 5'-Monophosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN SSM1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 26-280
    Gene: SSM1, SDT1, YGL224C
    Mutation: YES
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SDT1 NUCLEOTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2U5P1Ligand/IonURIDINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:38 , ASP A:203 , U5P A:265 , HOH A:294 , HOH A:304BINDING SITE FOR RESIDUE MG A 264
2AC2SOFTWAREILE A:37 , ASP A:38 , MET A:52 , TYR A:79 , LEU A:84 , ASP A:105 , THR A:140 , ASN A:141 , ALA A:142 , TYR A:168 , LYS A:177 , MG A:264 , HOH A:278 , HOH A:279 , HOH A:294 , HOH A:422BINDING SITE FOR RESIDUE U5P A 265

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:177 -Pro A:178

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OPX)

(-) 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:247
 aligned with SDT1_YEAST | P53078 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:256
                                                                                                                                                                                                                                                                                       280  
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276   |  
           SDT1_YEAST    27 HLESLTHPGSKVTFPIDQDISATPQNPNLKVFFFDIDNCLYKSSTRIHDLMQQSILRFFQTHLKLSPEDAHVLNNSYYKEYGLAIRGLVMFHKVNALEYNRLVDDSLPLQDILKPDIPLRNMLLRLRQSGKIDKLWLFTNAYKNHAIRCLRLLGIADLFDGLTYCDYSRTDTLVCKPHVKAFEKAMKESGLARYENAYFIDDSGKNIETGIKLGMKTCIHLVENEVNEILGQTPEGAIVISDILELPHVVSDLF--   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................-----........eeee.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh......eee..............hhhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh...eeeee......----......eee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3opx A   2 HLESLTHPGSKVTFPID-----TPQNPNLKVFFFAIDNCLYKSSTRIHDLMQQSILRFFQTHLKLSPEDAHVLNNSYYKEYGLAIRGLVMFHKVNALEYNRLVDDSLPLQDILKPDIPLRNMLLRLRQSGKIDKLWLFTNAYKNHAIRCLRLLGIADLFDGLTYCDYSRTDTLVCKPHVKAFEKAMKESGLARYENAYFIDDSGKNIETGIKLGMKTCIHLVENEVN----QTPEGAIVISDILELPHVVSDLFLE 257
                                    11      |  -  |     31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      |  - |     241       251      
                                           18    24                                                                                                                                                                                                         228  233
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  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 3OPX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

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