3C3I - JenaLib

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Title :   EVOLUTION OF CHLORELLA VIRUS DUTPASE

Authors :   M. Yamanishi, K. Homma, Y. Zhang, L. V. J. Etten, H. Moriyama

Date :   28 Jan 08 (Deposition) - 10 Feb 09 (Release) - 17 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (3x)
Biol. Unit 2: B,C,D  (1x)

Keywords :   Dutpase Chlorella Virus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Homma, H. Moriyama
Crystallization And Crystal-Packing Studies Of Chlorella Virus Deoxyuridine Triphosphatase.
Acta Crystallogr. , Sect. F V. 65 1030 2009
PubMed-ID: 19851015 | Reference-DOI: 10.1107/S1744309109034459
(for further references see the PDB file header)

Molecule 1 - DEOXYURIDINE TRIPHOSPHATASE
	Chains	:	A, B, C, D
	EC Number	:	3.6.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-23A
	Expression System Strain	:	BL21-DE3-PLYS
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	PARAMECIUM BURSARIA CHLORELLA VIRUS IL3A
	Strain	:	MU-22

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (3x)	:	A
Biological Unit 2 (1x)	:		B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	DUD	4	Ligand/Ion	DEOXYURIDINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	DUD	3	Ligand/Ion	DEOXYURIDINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	DUD	3	Ligand/Ion	DEOXYURIDINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:73	BINDING SITE FOR RESIDUE MG A 998
2	AC2	SOFTWARE	ASP B:73 , ASP D:73	BINDING SITE FOR RESIDUE MG D 999
3	AC3	SOFTWARE	ARG A:63 , SER A:64 , GLY A:65 , ALA A:76 , GLY A:77 , VAL A:78 , ILE A:79 , ASP A:80 , TYR A:83 , GLU A:86 , LYS A:88 , ILE A:90 , ARG C:97	BINDING SITE FOR RESIDUE DUD A 776
4	AC4	SOFTWARE	GLY B:77 , VAL B:78 , ILE B:79 , ASP B:80 , TYR B:83 , VAL B:87 , LYS B:88 , ILE B:90 , HOH B:781 , ARG C:131 , PHE C:136 , ARG D:63 , SER D:64 , GLY D:65	BINDING SITE FOR RESIDUE DUD B 777
5	AC5	SOFTWARE	ARG B:63 , SER B:64 , GLY B:65 , ALA C:76 , GLY C:77 , VAL C:78 , ILE C:79 , ASP C:80 , TYR C:83 , LYS C:88 , ARG D:131	BINDING SITE FOR RESIDUE DUD B 778
6	AC6	SOFTWARE	ARG B:131 , GLY B:135 , PHE B:136 , GLY B:137 , ARG C:63 , SER C:64 , GLY C:65 , GLU D:11 , ALA D:76 , GLY D:77 , VAL D:78 , ILE D:79 , ASP D:80 , TYR D:83 , LYS D:88	BINDING SITE FOR RESIDUE DUD B 779

(no "SS Bond" information available for 3C3I)

(no "Cis Peptide Bond" information available for 3C3I)

(no "SAP(SNP)/Variant" information available for 3C3I)

(no "PROSITE Motif" information available for 3C3I)

(no "Exon" information available for 3C3I)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:127
 aligned with Q5I3E5_PBCVI | Q5I3E5 from UniProtKB/TrEMBL  Length:141

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
         Q5I3E5_PBCVI     2 SSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDEDYTGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSD 128
               SCOP domains d3c3ia_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee...ee......eeeeeeee.....eee....eeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3i A   2 SSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDSDYRGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSD 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:136
 aligned with Q5I3E5_PBCVI | Q5I3E5 from UniProtKB/TrEMBL  Length:141

    Alignment length:136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      
         Q5I3E5_PBCVI     2 SSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDEDYTGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSDTARGSGGFG 137
               SCOP domains d3c3ib_ B: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........ee.......eeee....eee....ee.....eeee....eeeeee.hhhhhhhhheee...ee...........eee.....eee....eeeeeeeee.....eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3i B   2 SSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDSDYRGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSDTARGSGGFG 137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain C from PDB  Type:PROTEIN  Length:136
 aligned with Q5I3E5_PBCVI | Q5I3E5 from UniProtKB/TrEMBL  Length:141

    Alignment length:136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      
         Q5I3E5_PBCVI     2 SSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDEDYTGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSDTARGSGGFG 137
               SCOP domains d3c3ic_ C: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheeee..ee......eeeeeeee.....eee....eeeeeeeee.....eee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3i C   2 SSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDSDYRGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSDTARGSGGFG 137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain D from PDB  Type:PROTEIN  Length:130
 aligned with Q5I3E5_PBCVI | Q5I3E5 from UniProtKB/TrEMBL  Length:141

    Alignment length:130
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
         Q5I3E5_PBCVI     2 SSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDEDYTGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSDTAR 131
               SCOP domains d3c3id_ D: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.................eeee....eee....eeeee..eeee....eeeeee.hhhhhhh..eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3i D   2 SSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDSDYRGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLDLSDTAR 131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-clip (280)

Superfamily: dUTPase-like (122)

Family: automated matches (51)

Protein domain: automated matches (51)

Paramecium bursaria chlorella virus il3a [TaxId: 46019] (3)

1a	d3c3ia_	A:
1b	d3c3ib_	B:
1c	d3c3ic_	C:
1d	d3c3id_	D:

(no "CATH Domain" information available for 3C3I)

(no "Pfam Domain" information available for 3C3I)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q5I3E5_PBCVI | Q5I3E5)

molecular function
	GO:0004170	dUTP diphosphatase activity	Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
	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:0046080	dUTP metabolic process	The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.

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3c2t	CHLORELLA VIRUS IL-3A DUTPASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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