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(-) Description

Title :  CRYSTAL STRUCTURE OF Y116T/I16A DOUBLE MUTANT OF 5-HYDROXYISOURATE HYDROLASE IN COMPLEX WITH T4
 
Authors :  L. Cendron, I. Ramazzina, R. Percudani, G. Zanotti, R. Berni
Date :  17 Dec 10  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hiuase, Transthyretin, Trp, Thyroid Hormones, Molecular Evolution, Purine Metabolism, Greek Key Beta-Barrel, Hydrolase, Point Mutation, Peroxisome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Cendron, I. Ramazzina, R. Percudani, C. Rasore, G. Zanotti, R. Bern
Probing The Evolution Of Hydroxyisourate Hydrolase Into Transthyretin Through Active-Site Redesign
J. Mol. Biol. 2011
PubMed: search  |  Reference-DOI: 10.1016/J.JMB.2011.04.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5-HYDROXYISOURATE HYDROLASE
    Chains: A, B, C, D
    EC Number: 3.5.2.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B-HIUASE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN UNP 20-138
    Gene: URAH
    Mutation: YES
    Organism Common: ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: HIU HYDROLASE, HIUHASE, TRANSTHYRETIN-RELATED PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1T442Ligand/Ion3,5,3',5'-TETRAIODO-L-THYRONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:105 , SER A:114 , LEU C:14 , LEU C:107 , SER C:114BINDING SITE FOR RESIDUE T44 C 128
2AC2SOFTWAREHIS B:12 , PRO B:105 , SER B:114 , LEU D:14 , SER D:114BINDING SITE FOR RESIDUE T44 D 328

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q1E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q1E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q1E)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSTHYRETIN_1PS00768 Transthyretin signature 1.HIUH_DANRE31-46
 
 
 		  4A:12-27
B:12-27
C:12-27
D:12-27

(-) Exons   (0, 0)

(no "Exon" information available for 3Q1E)

(-) 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:113
 aligned with HIUH_DANRE | Q06S87 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:113
                                    35        45        55        65        75        85        95       105       115       125       135   
           HIUH_DANRE    26 SPLSTHVLNIAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTYRGS 138
               SCOP domains d3q1ea_ A: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eee....ee....eeeeeee......eeeeeeee...........hhhhh..eeeeeeehhhhhhhhh........eeeeeee......ee..eeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----TRANSTHYRETIN_1 -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3q1e A   7 SPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    16        26        36        46        56        66        76        86        96       106       116   


Chain B from PDB  Type:PROTEIN  Length:114
 aligned with HIUH_DANRE | Q06S87 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:114
                                    34        44        54        64        74        84        94       104       114       124       134    
           HIUH_DANRE    25 LSPLSTHVLNIAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTYRGS 138
               SCOP domains d3q1eb_ B: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..eee....ee....eeeeeee......eeeeeeee...........hhhhh..eeeeeeehhhhhhhhh........eeeeeee......ee..eee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TRANSTHYRETIN_1 -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3q1e B   6 LSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    15        25        35        45        55        65        75        85        95       105       115    


Chain C from PDB  Type:PROTEIN  Length:114
 aligned with HIUH_DANRE | Q06S87 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:114
                                    34        44        54        64        74        84        94       104       114       124       134    
           HIUH_DANRE    25 LSPLSTHVLNIAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTYRGS 138
               SCOP domains d3q1ec_ C: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..eee....ee....eeeeeee......eeeeeeee..................eeeeeeehhhhhhhhh........eeeeeee......ee..eee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TRANSTHYRETIN_1 -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3q1e C   6 LSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    15        25        35        45        55        65        75        85        95       105       115    


Chain D from PDB  Type:PROTEIN  Length:116
 aligned with HIUH_DANRE | Q06S87 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:116
                                    32        42        52        62        72        82        92       102       112       122       132      
           HIUH_DANRE    23 TLLSPLSTHVLNIAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTYRGS 138
               SCOP domains d3q1ed_ D: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Transthyretin-3q1eD01 D:7-118                                                                                   - Pfam domains (1)
           Pfam domains (2) ---Transthyretin-3q1eD02 D:7-118                                                                                   - Pfam domains (2)
           Pfam domains (3) ---Transthyretin-3q1eD03 D:7-118                                                                                   - Pfam domains (3)
           Pfam domains (4) ---Transthyretin-3q1eD04 D:7-118                                                                                   - Pfam domains (4)
         Sec.struct. author .....ee..eee....ee....eeeeeee......eeeeeeee...........hhhhh..eeeeeeehhhhhhhh.........eeeeeee......ee..eee...eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------TRANSTHYRETIN_1 -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3q1e D   4 TLLSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    13        23        33        43        53        63        73        83        93       103       113
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q1E)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Transthyretin (88)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (HIUH_DANRE | Q06S87)
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:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
    GO:0033971    hydroxyisourate hydrolase activity    Catalysis of the reaction: 5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate + H(+).
biological process
    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.
    GO:0019628    urate catabolic process    The chemical reactions and pathways resulting in the breakdown of urate, the anion of uric acid, 2,6,8-trioxypurine.
cellular component
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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  3q1e
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  HIUH_DANRE | Q06S87
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 Related Entries

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

UniProtKB/Swiss-Prot
        HIUH_DANRE | Q06S87: 2h1x 2h6u 3iwu 3iwv

(-) Related Entries Specified in the PDB File

2h1x CRYSTAL STRUCTURE OF 5-HYDROXYISOURATE HYDROLASE FROM ZEBRAFISH
2h6u CRYSTAL STRUCTURE OF 5-HYDROXYISOURATE HYDROLASE FROM ZEBRAFISH
3iwv CRYSTAL STRUCTURE OF Y116T/I16A DOUBLE MUTANT OF 5- HYDROXYISOURATE HYDROLASE FROM ZEBRAFISH