3IWU - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF Y116T/I16A DOUBLE MUTANT OF 5-HYDROXYISOURATE HYDROLASE

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

Date :   03 Sep 09 (Deposition) - 01 Sep 10 (Release) - 04 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E,F,G,H  (1x)

Keywords :   Hiuase, Transthyretin, Trp, Thyroid Hormones, Molecular Evolution, Hydrolase, Peroxisome, Purine Metabolism (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)

Molecule 1 - 5-HYDROXYISOURATE HYDROLASE
	Chains	:	A, B, C, D, E, F, G, H
	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
	Gene	:	URAH
	Mutation	:	YES
	Organism Common	:	ZEBRAFISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955
	Synonym	:	HIU HYDROLASE, HIUHASE, TRANSTHYRETIN-RELATED PROTEIN

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3IWU)

(no "Site" information available for 3IWU)

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

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

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

Asymmetric Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSTHYRETIN_1	PS00768	Transthyretin signature 1.	HIUH_DANRE	31-46	8	A:12-27 B:12-27 C:12-27 D:12-27 E:12-27 F:12-27 G:12-27 H:12-27

Biological Unit 1 (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 - - - -

Biological Unit 2 (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	- - - - E:12-27 F:12-27 G:12-27 H:12-27

(no "Exon" information available for 3IWU)

Asymmetric 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: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 d3iwua_ 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..eee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------TRANSTHYRETIN_1 -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3iwu A   6 LSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    15        25        35        45        55        65        75        85        95       105       115

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 d3iwub_ B: 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
                 3iwu 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 d3iwuc_ 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
                 3iwu C   6 LSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    15        25        35        45        55        65        75        85        95       105       115

Chain D 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 d3iwud_ D: 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
                 3iwu D   6 LSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    15        25        35        45        55        65        75        85        95       105       115

Chain E 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 d3iwue_ E: 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
                 3iwu E   6 LSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    15        25        35        45        55        65        75        85        95       105       115

Chain F 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 d3iwuf_ F: 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
                 3iwu F   6 LSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    15        25        35        45        55        65        75        85        95       105       115

Chain G 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 d3iwug_ G: 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
                 3iwu G   6 LSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    15        25        35        45        55        65        75        85        95       105       115

Chain H 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 d3iwuh_ H: 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
                 3iwu H   6 LSPLSTHVLNAAQGVPGANMTIVLHRLDPVSSAWNILTTGITNDDGRCPGLITKENFIAGVYKMRFETGKYWDALGETCFYPYVEIVFTITNTSQHYHVPLLLSRFSYSTTRGS 119
                                    15        25        35        45        55        65        75        85        95       105       115

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 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	d3iwua_	A:
1b	d3iwub_	B:
1c	d3iwuc_	C:
1d	d3iwud_	D:
1e	d3iwue_	E:
1f	d3iwuf_	F:
1g	d3iwug_	G:
1h	d3iwuh_	H:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G,H (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 Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3iwu)

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(no "Sites" information available for 3iwu)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3iwu)

Biological Units
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		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	3iwu
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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Access by UniProt ID/Accession number
	HIUH_DANRE \| Q06S87
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	3.5.2.17
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	HIUH_DANRE \| Q06S87
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UniProtKB/Swiss-Prot
	HIUH_DANRE \| Q06S87	:	2h1x 2h6u 3iwv 3q1e

2h1x	CRYSTAL STRUCTURE OF 5-HYDROXYISOURATE HYDROLASE FROM ZEBRA FISH
2h6u	CRYSTAL STRUCTURE OF 5-HYDROXYISOURATE HYDROLASE FROM ZEBRA FISH
3iwv

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