1SYL - JenaLib

Title :   CRYSTAL STRUCTURE OF INACTIVE MUTANT DUTPASE COMPLEXED WITH SUBSTRATE DUTP

Authors :   O. Barabas, J. Kovari, V. Pongracz, M. Wilmanns, B. G. Vertessy

Date :   01 Apr 04 (Deposition) - 07 Sep 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Enzyme-Ligand Complex, Jelly Roll, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Barabas, V. Pongracz, J. Kovari, M. Wilmanns, B. G. Vertessy
Structural Insights Into The Catalytic Mechanism Of Phosphate Ester Hydrolysis By Dutpase
J. Biol. Chem. V. 279 42907 2004
PubMed-ID: 15208312 | Reference-DOI: 10.1074/JBC.M406135200
(for further references see the PDB file header)

Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
	Chains	:	A
	EC Number	:	3.6.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DUT
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DUTPASE, DUTP PYROPHOSPHATASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DUT A:777 , HOH A:1010 , HOH A:1033 , HOH A:1083	BINDING SITE FOR RESIDUE MG A 997
2	AC2	SOFTWARE	MET A:68 , ARG A:71 , SER A:72 , GLY A:73 , ASN A:84 , GLY A:87 , LEU A:88 , ILE A:89 , ASN A:90 , TYR A:93 , MET A:98 , GLN A:119 , MG A:997 , HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1010 , HOH A:1012 , HOH A:1033 , HOH A:1038 , HOH A:1058 , HOH A:1083 , HOH A:1084 , HOH A:1095	BINDING SITE FOR RESIDUE DUT A 777
3	AC3	SOFTWARE	TRP A:102 , ARG A:104 , HOH A:1048 , HOH A:1102	BINDING SITE FOR RESIDUE TRS A 501
4	AC4	SOFTWARE	PRO A:124 , HOH A:1110 , HOH A:1140	BINDING SITE FOR RESIDUE TRS A 502

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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

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Chain A from PDB  Type:PROTEIN  Length:137
 aligned with DUT_ECOLI | P06968 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:137
                             1                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       
            DUT_ECOLI     - -MKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFD 136
               SCOP domains d1syla_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                     SCOP domains
               CATH domains 1sylA00 A:1-137  [code=2.70.40.10, no name defined]                                                                                       CATH domains
               Pfam domains ---------------dUTPase-1sylA01 A:16-137                                                                                                   Pfam domains
         Sec.struct. author .....eeee.....................eeee......eee....eeeeeeeeeee.....eeeeee.hhhhhhhhheee....eee......eeeeeeee.....eee....eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1syl A   1 MMKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLINSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFD 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (DUT_ECOLI | P06968)

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.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006226	dUMP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
	GO:0046081	dUTP catabolic process	The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate.
	GO:0046080	dUTP metabolic process	The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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