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(-) Description

Title :  CRYSTAL STRUCTURE OF ALLANTOICASE (YIR029W) FROM SACCHAROMYCES CEREVISIAE AT 2.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Aug 03  (Deposition) - 02 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Yir029W, Allantoicase, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, R. Schwarzenbacher, R. Page, E. Sims, P. Abdubek, E. Ambing, T. Biorac, L. S. Brinen, J. Cambell, J. M. Canaves, H. J. Chiu, X. Dai, A. M. Deacon, M. Didonato, M. A. Elsliger, R. Floyd, A. Godzik, C. Grittini, S. K. Grzechnik, E. Hampton, L. Jaroszewski, C. Karlak, H. E. Klock, E. Koesema, J. S. Kovarik, A. Kreusch, P. Kuhn, S. A. Lesley I. Levin, D. Mcmullan, T. M. Mcphillips, M. D. Miller, A. Morse, K. Moy, J. Ouyang, K. Quijano, R. Reyes, F. Rezezadeh, A. Robb, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, F. Von Delft, X. Wang, B. West, G. Wolf, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of An Allantoicase (Yir029W) From Saccharomyces Cerevisiae At 2. 4 A Resolution
Proteins V. 56 619 2004
PubMed-ID: 15229895  |  Reference-DOI: 10.1002/PROT.20164

(-) Compounds

Molecule 1 - ALLANTOICASE
    Chains: A
    EC Number: 3.5.3.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YIR029W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: ALLANTOATE AMIDINOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1O59)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O59)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:170 -Pro A:171
2Ile A:330 -Pro A:331

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O59)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O59)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIR029W1YIR029W.1IX:410804-4118351032ALLC_YEAST1-3433431A:1-343 (gaps)343

(-) 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:318
 aligned with ALLC_YEAST | P25335 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:344
                             1                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339    
           ALLC_YEAST     - -MKFFSLADEAEFKSIIISKNKAVDVIGSKLGGQVVSFSDEWFASAENLIQPTAPIRDPTRFVHSGAWYDGWETRRHNEMEYDWVIIKMGVAAAHIIGGEIDTAFFNGNHAPFVSIEALYDEGEEGNIVEDDSRWVEIVEKFECGPSQRHLFVRGNGLTKERFTHIKLKMYPDGGIARFRLYGRVVPPELKTKDHIIDLAYVCNGAVALKYSDQHFGSVDNLLLPGRGHDMSDGWETKRSRQPGHTDWAVIQLGRESSFIEKIIVDTAHFRGNFPQFITVEGCLKESESSENTGEGTWVELVGKSKTGPDKEHVYEIRKSIRVSHVKLTIIPDGGVKRIRVWGY 343
               SCOP domains d1o59a1 A:0-187 Allantoicase                                                                                                                                                                      d1o59a2 A:194-343 Allantoicase                                                                                                                         SCOP domains
               CATH domains --1o59A01 A:2-187 Galactose-binding domain-like                                                                                                                                                   1o59A02 A:194-343 Galactose-binding domain-like                                                                                                        CATH domains
           Pfam domains (1) ----------------------------------------------------------         -------------------------------------------------------------------------------------------------------------------------      ----------Allantoicase-1o59A01 A:204-342                                                                                                             - Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------         -------------------------------------------------------------------------------------------------------------------------      ----------Allantoicase-1o59A02 A:204-342                                                                                                             - Pfam domains (2)
         Sec.struct. author ..eeehhhhhhhhhhhhh.....ee..hhhhh.eeeee......hhhhhhh.......---------....ee.........eeeeee.....eeeeeeeee..........eeeeeee................eeeeeeee.....eeeee...........eeeeeee...ee.eeeeeeee...------..ee..hhhhh.eeeee....ee.hhhhhh.....hhhh.ee..........eeeeee......eeeeeeee..........eeeeeee..-----------.eeeeeeeee.....eeeeeeeee....eeeeeee...ee.eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 -Exon 1.1  PDB: A:1-343 (gaps) UniProt: 1-343                                                                                                                                                                                                                                                                                                            Transcript 1
                 1o59 A   0 HmKFFSLADEAEFKSIIISKNKAVDVIGSKLGGQVVSFSDEWFASAENLIQPTAPIRD---------WYDGWETRRHNEmEYDWVIIKmGVAAAHIIGGEIDTAFFNGNHAPFVSIEALYDEGEEGNIVEDDSRWVEIVEKFECGPSQRHLFVRGNGLTKERFTHIKLKmYPDGGIARFRLYGRVVPP------HIIDLAYVCNGAVALKYSDQHFGSVDNLLLPGRGHDmSDGWETKRSRQPGHTDWAVIQLGRESSFIEKIIVDTAHFRGNFPQFITVEGCLK-----------TWVELVGKSKTGPDKEHVYEIRKSIRVSHVKLTIIPDGGVKRIRVWGY 343
                             |       9        19        29        39        49       | -       |69        79        89        99       109       119       129       139       149       159       169       179       | -    |  199       209       219       229|      239       249       259       269       279    |    -      |299       309       319       329       339    
                             |                                                      57        67          79-MSE   88-MSE                                                                          169-MSE           187    194                                 230-MSE                                               284         296                                               
                             1-MSE
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ALLC_YEAST | P25335)
molecular function
    GO:0004037    allantoicase activity    Catalysis of the reaction: allantoate + H(2)O = (S)-ureidoglycolate + urea.
    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.
biological process
    GO:0000256    allantoin catabolic process    The chemical reactions and pathways resulting in the breakdown of allantoin, (2,5-dioxo-4-imidazolidinyl)urea.
    GO:0006144    purine nucleobase metabolic process    The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
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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  1o59
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALLC_YEAST | P25335: 1sg3

(-) Related Entries Specified in the PDB File

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