1PKH - JenaLib

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Title :   STRUCTURAL BASIS FOR RECOGNITION AND CATALYSIS BY THE BIFUNCTIONAL DCTP DEAMINASE AND DUTPASE FROM METHANOCOCCUS JANNASCHII

Authors :   J. L. Huffman, H. Li, R. H. White, J. A. Tainer

Date :   05 Jun 03 (Deposition) - 19 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.42

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

Keywords :   Dctp Deaminase, Dutpase, Dcd-Dut, Mj0430, Dctp, Dutp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. L. Huffman, H. Li, R. H. White, J. A. Tainer
Structural Basis For Recognition And Catalysis By The Bifunctional Dctp Deaminase And Dutpase From Methanococcus Jannaschii
J. Mol. Biol. V. 331 885 2003
PubMed-ID: 12909016 | Reference-DOI: 10.1016/S0022-2836(03)00789-7
(for further references see the PDB file header)

Molecule 1 - BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.5.4.13, 3.6.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	BL21 (DE3) RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MJ0430
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	MJDCD-DUT, DCD/DUT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 9)

No.	Name	Count	Type	Full Name
1	EDO	9	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 9)

No.	Name	Count	Type	Full Name
1	EDO	9	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:139 , GLU B:76 , ILE B:79 , ASN B:80 , LYS B:83 , HOH B:415	BINDING SITE FOR RESIDUE EDO B 205
2	AC2	SOFTWARE	ASP B:25 , PHE B:26 , VAL B:27 , GLY B:28 , ASP B:33 , ARG B:160	BINDING SITE FOR RESIDUE EDO B 206
3	AC3	SOFTWARE	ASP A:25 , PHE A:26 , VAL A:27 , ASP A:33 , ARG A:160 , ASN B:87 , HOH B:504	BINDING SITE FOR RESIDUE EDO A 205
4	AC4	SOFTWARE	GLU B:39 , ILE B:41 , LEU B:97 , GLY B:98 , THR B:99	BINDING SITE FOR RESIDUE EDO B 207
5	AC5	SOFTWARE	ASP A:174 , TYR A:177 , SER A:178 , HOH A:433 , LYS B:60 , LYS B:62 , HOH B:338	BINDING SITE FOR RESIDUE EDO A 206
6	AC6	SOFTWARE	ARG B:16 , GLU B:105 , LEU B:106 , PRO B:107 , HOH B:286 , HOH B:453	BINDING SITE FOR RESIDUE EDO B 208
7	AC7	SOFTWARE	PRO A:21 , ASN A:23 , THR A:35 , GLU A:102 , HOH A:404	BINDING SITE FOR RESIDUE EDO A 207
8	AC8	SOFTWARE	GLY B:37 , ASP B:38 , ASN B:101 , LYS B:157 , ASN B:158	BINDING SITE FOR RESIDUE EDO B 209
9	AC9	SOFTWARE	THR B:35 , HOH B:501	BINDING SITE FOR RESIDUE EDO B 210

(no "SS Bond" information available for 1PKH)

Asymmetric Unit

No.	Residues
1	Lys A:20	-	Pro A:21
2	Lys B:20	-	Pro B:21

(no "SAP(SNP)/Variant" information available for 1PKH)

(no "PROSITE Motif" information available for 1PKH)

(no "Exon" information available for 1PKH)

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:182
 aligned with DCD_METJA | Q57872 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
            DCD_METJA     1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERKT 182
               SCOP domains d1pkha_ A: Bifunctional dCTP deaminase/dUTPase                                                                                                                                         SCOP domains
               CATH domains 1pkhA00 A:1-182  [code=2.70.40.10, no name defined]                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eee..hhhhh....eeee...eeeee............eeeee...eeeee......hhhhhhhhhhhhh..eeee..eeeeeeeeee....eeeeeeehhhhhh..ee......ee....eeeeeeeeee....eeee...eeeeeeeee........eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pkh A   1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERKT 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with DCD_METJA | Q57872 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
            DCD_METJA     1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADV 175
               SCOP domains d1pkhb_ B: Bifunctional dCTP deaminase/dUTPase                                                                                                                                  SCOP domains
               CATH domains 1pkhB00 B:1-175  [code=2.70.40.10, no name defined]                                                                                                                             CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------dUTPase-1pkhB01 B:85-175                                                                    Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------dUTPase-1pkhB02 B:85-175                                                                    Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhh...eee..hhh.ee..eeeee...eeeee............eeeeee..eeeee......hhhhhhhhhhhhh..eeee..eeeeeeeeee....eeeeeeehhhhhh..ee......ee....eeeeeeeeee....eeee...eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pkh B   1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADV 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: beta-clip (280)

Superfamily: dUTPase-like (122)

Family: dUTPase-like (71)

Protein domain: Bifunctional dCTP deaminase/dUTPase (6)

Methanococcus jannaschii [TaxId: 2190] (6)

1a	d1pkha_	A:
1b	d1pkhb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A (52)

Homologous Superfamily: [code=2.70.40.10, no name defined] (51)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (4)

1a	1pkhB00	B:1-175
1b	1pkhA00	A:1-182

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: dUTPase (38)

Family: dUTPase (38)

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth (4)

1a	dUTPase-1pkhB01	B:85-175
1b	dUTPase-1pkhB02	B:85-175

Asymmetric Unit(hide GO term definitions)

Chain A,B (DCD_METJA | Q57872)

molecular function
	GO:0033973	dCTP deaminase (dUMP-forming) activity	Catalysis of the reaction: dCTP + 2 H(2)O = diphosphate + dUMP + H(+) + NH(4)(+).
	GO:0008829	dCTP deaminase activity	Catalysis of the reaction: dCTP + H2O = dUTP + NH3.
	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:0006226	dUMP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
	GO:0006229	dUTP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUTP, deoxyuridine (5'-)triphosphate.
	GO:0046080	dUTP metabolic process	The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	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:0009220	pyrimidine ribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	DCD_METJA \| Q57872	:	1ogh 1pkj 1pkk 2hxb 2hxd 3gf0

1pkj	BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE COMPLEXED WITH DEOXYURIDINE 5'-TRIPHOSPHATE
1pkk	BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE COMPLEXED WITH 2'- DEOXYCYTIDINE-5'-TRIPHOSPHATE

Description

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Ligands, Modified Residues, Ions (1, 9)

Sites (9, 9)

SS Bonds (0, 0)

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