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(-) Description

Title :  CRYSTAL STRUCTURE OF 5'-NUCLEOTIDASE SDT1 FROM SACCHAROMYCES CEREVISIAE
 
Authors :  M. K. Teng, L. W. Niu, N. Shi
Date :  30 Aug 10  (Deposition) - 02 Mar 11  (Release) - 02 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Shi, M. K. Teng, L. W. Niu
Crystal Structure Of The First Pyrimidine 5'-Nucleotidase Sdt1 From Saccharomyces Cerevisiae
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
    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  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL5Ligand/IonGLYCEROL
3IOD4Ligand/IonIODIDE ION
4MG1Ligand/IonMAGNESIUM ION
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:36 , ILE A:37 , ASP A:38 , THR A:140 , ASN A:141 , ALA A:142 , LYS A:177 , MG A:276 , HOH A:277 , HOH A:379BINDING SITE FOR RESIDUE PO4 A 264
02AC2SOFTWARELEU A:64 , LEU A:66 , HIS A:93 , GOL A:266 , HOH A:395BINDING SITE FOR RESIDUE GOL A 265
03AC3SOFTWAREGOL A:265 , HOH A:343 , HOH A:433BINDING SITE FOR RESIDUE GOL A 266
04AC4SOFTWAREARG A:58 , GLN A:61 , THR A:62 , ARG A:128 , ILE A:133 , ASP A:134 , HOH A:287BINDING SITE FOR RESIDUE GOL A 267
05AC5SOFTWARESER A:44 , GLU A:224 , ASN A:225 , GLU A:226 , HOH A:371 , HOH A:373BINDING SITE FOR RESIDUE GOL A 268
06AC6SOFTWAREILE A:113 , LEU A:114 , LYS A:115 , PRO A:116 , ASP A:117 , HOH A:374 , HOH A:386BINDING SITE FOR RESIDUE GOL A 269
07AC7SOFTWAREASN A:27 , LEU A:51 , SER A:55 , ARG A:58 , SER A:107 , LEU A:108 , PRO A:109 , HOH A:383BINDING SITE FOR RESIDUE ACT A 270
08AC8SOFTWAREGLY A:205 , LYS A:206 , GLU A:209 , GLY A:232 , GLN A:233BINDING SITE FOR RESIDUE ACT A 271
09AC9SOFTWARELEU A:3 , GLN A:111 , ARG A:149 , HOH A:415BINDING SITE FOR RESIDUE IOD A 273
10BC1SOFTWAREHOH A:396BINDING SITE FOR RESIDUE IOD A 274
11BC2SOFTWAREASP A:167 , LYS A:185 , HOH A:416BINDING SITE FOR RESIDUE IOD A 275
12BC3SOFTWAREASP A:36 , ASP A:38 , ASP A:203 , PO4 A:264 , HOH A:452 , HOH A:453BINDING SITE FOR RESIDUE MG A 276

(-) SS Bonds  (0, 0)

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

(-) 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 3ONN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ONN)

(-) 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:249
 aligned with SDT1_YEAST | P53078 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:255
                                                                                                                                                                                                                                                                                      280  
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277  |  
           SDT1_YEAST    28 LESLTHPGSKVTFPIDQDISATPQNPNLKVFFFDIDNCLYKSSTRIHDLMQQSILRFFQTHLKLSPEDAHVLNNSYYKEYGLAIRGLVMFHKVNALEYNRLVDDSLPLQDILKPDIPLRNMLLRLRQSGKIDKLWLFTNAYKNHAIRCLRLLGIADLFDGLTYCDYSRTDTLVCKPHVKAFEKAMKESGLARYENAYFIDDSGKNIETGIKLGMKTCIHLVENEVNEILGQTPEGAIVISDILELPHVVSDLF--   -
               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.....hhhhh......eee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3onn A   3 LESLTHPGSKVTFPID-----TPQNPNLKVFFFDIDNCLYKSSTRIHDLMQQSILRFFQTHLKLSPEDAHVLNNSYYKEYGLAIRGLVMFHKVNALEYNRLVDDSLPLQDILKPDIPLRNMLLRLRQSGKIDKLWLFTNAYKNHAIRCLRLLGIADLFDGLTYCDYSRT-TLVCKPHVKAFEKAMKESGLARYENAYFIDDSGKNIETGIKLGMKTCIHLVENEVNEILGQTPEGAIVISDILELPHVVSDLFLE 257
                                    12     |   - |      32        42        52        62        72        82        92       102       112       122       132       142       152       162        |-|      182       192       202       212       222       232       242       252     
                                          18    24                                                                                                                                                171 |                                                                                    
                                                                                                                                                                                                    173
   Legend:   → Mismatch (orange background)
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  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 3ONN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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

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

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

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