1RN8 - JenaLib

Title :   CRYSTAL STRUCTURE OF DUTPASE COMPLEXED WITH SUBSTRATE ANALOGUE IMIDO-DUTP

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

Date :   01 Dec 03 (Deposition) - 07 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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

Keywords :   Jelly Roll, Enzyme-Ligand Complex, 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, DNAS, SOF, B3640
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DUTPASE, DUTP PYROPHOSPHATASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	DUP	1	Ligand/Ion	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (3, 9)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	DUP	3	Ligand/Ion	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DUP A:777 , HOH A:1019 , HOH A:1045 , HOH A:1079	BINDING SITE FOR RESIDUE MG A 999
2	AC2	SOFTWARE	ARG A:34 , GLU A:115 , ARG A:116 , HOH A:1026 , HOH A:1044 , HOH A:1106 , HOH A:1119	BINDING SITE FOR RESIDUE ACT A 801
3	AC3	SOFTWARE	MET A:68 , ARG A:71 , SER A:72 , GLY A:73 , ASN A:84 , GLY A:87 , LEU A:88 , ASP A:90 , TYR A:93 , MET A:98 , GLN A:119 , MG A:999 , HOH A:1000 , HOH A:1001 , HOH A:1014 , HOH A:1019 , HOH A:1020 , HOH A:1027 , HOH A:1045 , HOH A:1050 , HOH A:1051 , HOH A:1056 , HOH A:1065 , HOH A:1069 , HOH A:1073 , HOH A:1079 , HOH A:1149	BINDING SITE FOR RESIDUE DUP A 777
4	AC4	SOFTWARE	TRP A:102 , ARG A:104 , HOH A:1043 , HOH A:1097	BINDING SITE FOR RESIDUE TRS A 800

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:140
 aligned with DUT_ECOLI | P06968 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:152
                             1                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
            DUT_ECOLI     - -MKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFDATDRGEGGFGHSGRQ 151
               SCOP domains d1rn8a_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                                    SCOP domains
               CATH domains 1rn8A00 A:1-152  [code=2.70.40.10, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------dUTPase-1rn8A01 A:16-146                                                                                                               -- 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
                 1rn8 A   1 MMKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFD--------F----RQ 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |  -     |   -| 
                                                                                                                                                                  137      146  151

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	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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