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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PUTATIVE UREIDOGLYCOLATE HYDROLASE PP4288 FROM PSEUDOMONAS PUTIDA, NORTHEAST STRUCTURAL GENOMICS TARGET PPR49
 
Authors :  F. Forouhar, M. Abashidze, S. Jayaraman, C. K. Ho, K. Conover, T. B. Acto G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomic Consortium (Nesg)
Date :  20 Oct 05  (Deposition) - 15 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  All Beta Protein, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, M. Abashidze, S. Jayaraman, C. K. Ho, K. Conover, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Putative Ureidoglycolate Hydrolase Pp4288 From Pseudomonas Putida, Northeast Structural Genomics Target Ppr49
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UREIDOGLYCOLATE HYDROLASE
    Chains: A, B
    EC Number: 3.5.3.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: XL-10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ALLA
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric/Biological Unit (2, 17)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2NA3Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE A:66 , PRO A:67 , CYS A:150 , HOH A:476 , HOH A:482BINDING SITE FOR RESIDUE NA A 401
2AC2SOFTWAREGLU A:74 , HIS A:76 , GLN A:81 , HIS A:126 , HOH A:473 , HOH A:487BINDING SITE FOR RESIDUE NA A 402
3AC3SOFTWAREASN A:148 , ASP A:151 , HOH A:434 , HOH A:452 , HOH A:470BINDING SITE FOR RESIDUE NA A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BDR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Mse A:66 -Pro A:67
2Mse B:66 -Pro B:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BDR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BDR)

(-) Exons   (0, 0)

(no "Exon" information available for 2BDR)

(-) 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:166
 aligned with ALLA_PSEPK | P59285 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      
           ALLA_PSEPK     1 MRTLMIEPLTKEAFAQFGDVIETDGSDHFMINNGSTMRFHKLATVETAEPEDKAIISIFRADAQDMPLTVRMLERHPLGSQAFIPLLGNPFLIVVAPVGDAPVSGLVRAFRSNGRQGVNYHRGVWHHPVLTIEKRDDFLVVDRSGSGNNCDEHYFTEEQMLILNPH 166
               SCOP domains d2bdra1 A:1-166 Ureidoglycolate hydrolase AllA                                                                                                                         SCOP domains
               CATH domains -2bdrA00 A:2-166 Ureidoglycolate hydrolase                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eee.hhhhhh..eeee.......eee....eeeeeeeeee.......eeeeeeeeee.....eee.eeee.....eeeee.....eeeeee......hhhhheeeee....eeee....ee...ee...eeeeeeeeee......eeee.hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bdr A   1 mRTLmIEPLTKEAFAQFGDVIETDGSDHFmINNGSTmRFHKLATVETAEPEDKAIISIFRADAQDmPLTVRmLERHPLGSQAFIPLLGNPFLIVVAPVGDAPVSGLVRAFRSNGRQGVNYHRGVWHHPVLTIEKRDDFLVVDRSGSGNNCDEHYFTEEQmLILNPH 166
                            |   |   10        20        30      | 40        50        60     |  70 |      80        90       100       110       120       130       140       150       160      
                            |   |                       30-MSE 37-MSE                       66-MSE |                                                                                     160-MSE  
                            1-MSE                                                                 72-MSE                                                                                          
                                5-MSE                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with ALLA_PSEPK | P59285 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      
           ALLA_PSEPK     1 MRTLMIEPLTKEAFAQFGDVIETDGSDHFMINNGSTMRFHKLATVETAEPEDKAIISIFRADAQDMPLTVRMLERHPLGSQAFIPLLGNPFLIVVAPVGDAPVSGLVRAFRSNGRQGVNYHRGVWHHPVLTIEKRDDFLVVDRSGSGNNCDEHYFTEEQMLILNPH 166
               SCOP domains d2bdrb_ B: Ureidoglycolate hydrolase AllA                                                                                                                              SCOP domains
               CATH domains -2bdrB00 B:2-166 Ureidoglycolate hydrolase                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eee.hhhhhh..eeee.......eee....eeeeeeeeee.......eeeeeeeeee.....eee.eeee.....eeeee.....eeeeee......hhhhheeeee....eeee....ee...ee...eeeeeeeeee......eeee.hhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bdr B   1 mRTLmIEPLTKEAFAQFGDVIETDGSDHFmINNGSTmRFHKLATVETAEPEDKAIISIFRADAQDmPLTVRmLERHPLGSQAFIPLLGNPFLIVVAPVGDAPVSGLVRAFRSNGRQGVNYHRGVWHHPVLTIEKRDDFLVVDRSGSGNNCDEHYFTEEQmLILNPH 166
                            |   |   10        20        30      | 40        50        60     |  70 |      80        90       100       110       120       130       140       150       160      
                            1-MSE                       30-MSE 37-MSE                       66-MSE |                                                                                     160-MSE  
                                5-MSE                                                             72-MSE
   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  (2, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BDR)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ALLA_PSEPK | P59285)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004848    ureidoglycolate hydrolase activity    Catalysis of the reaction: (S)-ureidoglycolate + H(2)O + 2 H(+) = CO(2) + glyoxylate + 2 NH(4)(+).
    GO:0050385    ureidoglycolate lyase activity    Catalysis of the reaction: (S)-ureidoglycolate = glyoxylate + urea.
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:0006145    purine nucleobase catabolic process    The chemical reactions and pathways resulting in the breakdown of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
    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.

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