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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)

Authors :   G. Zanotti, L. Cendron, C. Folli, I. Ramazzina, R. Percudani, R. Berni

Date :   17 May 06 (Deposition) - 31 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   5-Hydroxyisourate Hydrolase, Trp, Uric Acid Degradation, Allantoin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Zanotti, L. Cendron, I. Ramazzina, C. Folli, R. Percudani, R. Berni
Structure Of Zebra Fish Hiuase: Insights Into Evolution Of An Enzyme To A Hormone Transporter.
J. Mol. Biol. V. 363 1 2006
PubMed-ID: 16952372 | Reference-DOI: 10.1016/J.JMB.2006.07.079
(for further references see the PDB file header)

Molecule 1 - 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	ZEBRAFISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2H1X)

(no "Site" information available for 2H1X)

(no "SS Bond" information available for 2H1X)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Ser B:7	-	Pro B:8
3	Ser C:7	-	Pro C:8
4	Ser D:7	-	Pro D:8

(no "SAP(SNP)/Variant" information available for 2H1X)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSTHYRETIN_1	PS00768	Transthyretin signature 1.	HIUH_DANRE	31-46	4	A:12-27 B:12-27 C:12-27 D:12-27

(no "Exon" information available for 2H1X)

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 d2h1xa_ A: automated matches                                                                                      SCOP domains
               CATH domains 2h1xA00 A:7-119  [code=2.60.40.180, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eee....ee....eeeeeee......eeeeeeee..................eeeeeeehhhhhhhh.........eeeeeee......ee..eee...eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----TRANSTHYRETIN_1 -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2h1x A   7 SPLSTHVLNIAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTYRGS 119
                                    16        26        36        46        56        66        76        86        96       106       116

Chain B 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 d2h1xb_ B: automated matches                                                                                      SCOP domains
               CATH domains 2h1xB00 B:7-119  [code=2.60.40.180, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eee....ee....eeeeeee......eeeeeeee...........hhhhh..eeeeeeehhhhhhhh.........eeeeeee......ee..eeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----TRANSTHYRETIN_1 -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2h1x B   7 SPLSTHVLNIAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTYRGS 119
                                    16        26        36        46        56        66        76        86        96       106       116

Chain C 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 d2h1xc_ C: automated matches                                                                                      SCOP domains
               CATH domains 2h1xC00 C:7-119  [code=2.60.40.180, no name defined]                                                              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
                 2h1x C   7 SPLSTHVLNIAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTYRGS 119
                                    16        26        36        46        56        66        76        86        96       106       116

Chain D 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 d2h1xd_ D: automated matches                                                                                      SCOP domains
               CATH domains 2h1xD00 D:7-119  [code=2.60.40.180, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eee....ee....eeeeeee......eeeeeeee..................eeeeeeehhhhhhhh.........eeeeeee......ee..eeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----TRANSTHYRETIN_1 -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2h1x D   7 SPLSTHVLNIAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTYRGS 119
                                    16        26        36        46        56        66        76        86        96       106       116

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Prealbumin-like (433)

Superfamily: Transthyretin (synonym: prealbumin) (211)

Family: automated matches (13)

Protein domain: automated matches (13)

Zebrafish (Danio rerio) [TaxId: 7955] (5)

1a	d2h1xa_	A:
1b	d2h1xb_	B:
1c	d2h1xc_	C:
1d	d2h1xd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.180, no name defined] (150)

Zebrafish (Danio rerio) (2)

1a	2h1xA00	A:7-119
1b	2h1xC00	C:7-119
1c	2h1xD00	D:7-119
1d	2h1xB00	B:7-119

(no "Pfam Domain" information available for 2H1X)

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2h1x)

	Sites
(no "Sites" information available for 2h1x)

	Cis Peptide Bonds
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser B:7 - Pro B:8	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]
		Ser D:7 - Pro D:8	[ RasMol ]

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	HIUH_DANRE \| Q06S87	:	2h6u 3iwu 3iwv 3q1e

1f41	TRANSTHYRETIN (HUMAN)

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (4, 4)

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