3S86 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TM0159 WITH BOUND IMP

Authors :   M. Sommerhalter, C. Smith, K. Awwad, A. Desai

Date :   27 May 11 (Deposition) - 06 Jun 12 (Release) - 20 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Long Twisted Beta Strand Covered By Two Lobes, Non-Canonical Nucleoside Triphosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Awwad, A. Desai, C. Smith, M. Sommerhalter
Structural And Functional Characterization Of A Noncanonica Nucleoside Triphosphate Pyrophosphatase From Thermotoga Maritima.
Acta Crystallogr. , Sect. D V. 69 184 2013
PubMed-ID: 23385455 | Reference-DOI: 10.1107/S0907444912044630

Molecule 1 - NUCLEOSIDE-TRIPHOSPHATASE
	Chains	:	A, B, C, D
	EC Number	:	3.6.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMH1
	Expression System Strain	:	DL41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM_0159
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	NUCLEOSIDE TRIPHOSPHATE PHOSPHOHYDROLASE, NTPASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	IMP	4	Ligand/Ion	INOSINIC ACID
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:15 , LYS A:52 , ASP A:67 , ASP A:68 , SER A:69 , GLY A:70 , SER A:84 , ALA A:85 , TYR A:93 , PHE A:113 , PHE A:148 , GLY A:149 , TYR A:150 , ASP A:151 , LYS A:170 , HIS A:175 , ARG A:176 , SO4 A:198 , HOH A:237	BINDING SITE FOR RESIDUE IMP A 197
2	AC2	SOFTWARE	THR A:10 , THR A:11 , LYS A:15 , LYS A:52 , ASP A:67 , IMP A:197 , HOH A:221	BINDING SITE FOR RESIDUE SO4 A 198
3	AC3	SOFTWARE	LYS B:15 , GLU B:40 , ASP B:68 , SER B:69 , GLY B:70 , SER B:84 , ALA B:85 , TYR B:93 , PHE B:113 , PHE B:148 , GLY B:149 , TYR B:150 , ASP B:151 , LYS B:170 , HIS B:175 , ARG B:176 , SO4 B:198 , HOH B:244 , HOH B:250	BINDING SITE FOR RESIDUE IMP B 197
4	AC4	SOFTWARE	THR B:10 , THR B:11 , ASN B:12 , LYS B:15 , GLU B:40 , LYS B:52 , ASP B:67 , IMP B:197 , HOH B:220 , HOH B:250 , HOH B:253	BINDING SITE FOR RESIDUE SO4 B 198
5	AC5	SOFTWARE	LYS C:15 , GLU C:40 , ASP C:68 , SER C:69 , GLY C:70 , SER C:84 , ALA C:85 , TYR C:93 , PHE C:113 , PHE C:148 , GLY C:149 , TYR C:150 , ASP C:151 , LYS C:170 , HIS C:175 , ARG C:176 , SO4 C:198 , HOH C:203 , HOH C:224	BINDING SITE FOR RESIDUE IMP C 197
6	AC6	SOFTWARE	THR C:10 , THR C:11 , ASN C:12 , LYS C:15 , GLU C:40 , LYS C:52 , ASP C:67 , IMP C:197 , HOH C:224	BINDING SITE FOR RESIDUE SO4 C 198
7	AC7	SOFTWARE	LYS D:15 , GLU D:40 , LYS D:52 , ASP D:68 , SER D:69 , GLY D:70 , SER D:84 , ALA D:85 , TYR D:93 , PHE D:113 , PHE D:148 , GLY D:149 , TYR D:150 , ASP D:151 , LYS D:170 , HIS D:175 , ARG D:176 , SO4 D:198 , HOH D:217 , HOH D:234	BINDING SITE FOR RESIDUE IMP D 197
8	AC8	SOFTWARE	THR D:10 , THR D:11 , LYS D:15 , GLU D:40 , LYS D:52 , ASP D:67 , IMP D:197 , HOH D:234	BINDING SITE FOR RESIDUE SO4 D 198

(no "SS Bond" information available for 3S86)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:79	-	Pro A:80
2	Phe B:79	-	Pro B:80
3	Phe C:79	-	Pro C:80
4	Phe D:79	-	Pro D:80

(no "SAP(SNP)/Variant" information available for 3S86)

(no "PROSITE Motif" information available for 3S86)

(no "Exon" information available for 3S86)

Asymmetric/Biological 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:189
 aligned with IXTPA_THEMA | Q9WY06 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:189
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
          IXTPA_THEMA     3 KLTVYLATTNPHKVEEIKMIAPEWMEILPSPEKIEVVEDGETFLENSVKKAVVYGKKLKHPVMADDSGLVIYSLGGFPGVMSARFMEEHSYKEKMRTILKMLEGKDRRAAFVCSATFFDPVENTLISVEDRVEGRIANEIRGTGGFGYDPFFIPDGYDKTFGEIPHLKEKISHRSKAFRKLFSVLEKIL 191
               SCOP domains d3s86a_ A: Putative inosine/xanthosine triphosphate pyrophosphatase TM0159                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhh.....eeeee............hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh.......hhhhhhhhhhhhh.....eeeeeeeeeeee....eeeeeeeeeeeee...........hhh.eee...........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s86 A   3 KLTVYLATTNPHKVEEIKMIAPEWMEILPSPEKIEVVEDGETFLENSVKKAVVYGKKLKHPVMADDSGLVIYSLGGFPGVMSARFMEEHSYKEKMRTILKMLEGKDRRAAFVCSATFFDPVENTLISVEDRVEGRIANEIRGTGGFGYDPFFIPDGYDKTFGEIPHLKEKISHRSKAFRKLFSVLEKIL 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:189
 aligned with IXTPA_THEMA | Q9WY06 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:189
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
          IXTPA_THEMA     3 KLTVYLATTNPHKVEEIKMIAPEWMEILPSPEKIEVVEDGETFLENSVKKAVVYGKKLKHPVMADDSGLVIYSLGGFPGVMSARFMEEHSYKEKMRTILKMLEGKDRRAAFVCSATFFDPVENTLISVEDRVEGRIANEIRGTGGFGYDPFFIPDGYDKTFGEIPHLKEKISHRSKAFRKLFSVLEKIL 191
               SCOP domains d3s86b_ B: Putative inosine/xanthosine triphosphate pyrophosphatase TM0159                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhh....eeeee............hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh.......hhhhhhhhhhhhh.....eeeeeeeeeeee....eeeeeeeeeeeee...........hhh.eee.........hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s86 B   3 KLTVYLATTNPHKVEEIKMIAPEWMEILPSPEKIEVVEDGETFLENSVKKAVVYGKKLKHPVMADDSGLVIYSLGGFPGVMSARFMEEHSYKEKMRTILKMLEGKDRRAAFVCSATFFDPVENTLISVEDRVEGRIANEIRGTGGFGYDPFFIPDGYDKTFGEIPHLKEKISHRSKAFRKLFSVLEKIL 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain C from PDB  Type:PROTEIN  Length:189
 aligned with IXTPA_THEMA | Q9WY06 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:189
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
          IXTPA_THEMA     3 KLTVYLATTNPHKVEEIKMIAPEWMEILPSPEKIEVVEDGETFLENSVKKAVVYGKKLKHPVMADDSGLVIYSLGGFPGVMSARFMEEHSYKEKMRTILKMLEGKDRRAAFVCSATFFDPVENTLISVEDRVEGRIANEIRGTGGFGYDPFFIPDGYDKTFGEIPHLKEKISHRSKAFRKLFSVLEKIL 191
               SCOP domains d3s86c_ C: Putative inosine/xanthosine triphosphate pyrophosphatase TM0159                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhh.....eeeee............hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh.......hhhhhhhhhhhhhh....eeeeeeeeeeee....eeeeeeeeeeeee...........hhh.eee.........hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s86 C   3 KLTVYLATTNPHKVEEIKMIAPEWMEILPSPEKIEVVEDGETFLENSVKKAVVYGKKLKHPVMADDSGLVIYSLGGFPGVMSARFMEEHSYKEKMRTILKMLEGKDRRAAFVCSATFFDPVENTLISVEDRVEGRIANEIRGTGGFGYDPFFIPDGYDKTFGEIPHLKEKISHRSKAFRKLFSVLEKIL 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain D from PDB  Type:PROTEIN  Length:189
 aligned with IXTPA_THEMA | Q9WY06 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:189
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
          IXTPA_THEMA     3 KLTVYLATTNPHKVEEIKMIAPEWMEILPSPEKIEVVEDGETFLENSVKKAVVYGKKLKHPVMADDSGLVIYSLGGFPGVMSARFMEEHSYKEKMRTILKMLEGKDRRAAFVCSATFFDPVENTLISVEDRVEGRIANEIRGTGGFGYDPFFIPDGYDKTFGEIPHLKEKISHRSKAFRKLFSVLEKIL 191
               SCOP domains d3s86d_ D: Putative inosine/xanthosine triphosphate pyrophosphatase TM0159                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..hhhhh.......hhhhhhhhhhhhhh....eeeeeeeeeeee....eeeeeeeeeeeee...........hhh.eee.........hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s86 D   3 KLTVYLATTNPHKVEEIKMIAPEWMEILPSPEKIEVVEDGETFLENSVKKAVVYGKKLKHPVMADDSGLVIYSLGGFPGVMSARFMEEHSYKEKMRTILKMLEGKDRRAAFVCSATFFDPVENTLISVEDRVEGRIANEIRGTGGFGYDPFFIPDGYDKTFGEIPHLKEKISHRSKAFRKLFSVLEKIL 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Anticodon-binding domain-like (97)

Superfamily: ITPase-like (32)

Family: ITPase (Ham1) (12)

Protein domain: Putative inosine/xanthosine triphosphate pyrophosphatase TM0159 (2)

Thermotoga maritima [TaxId: 2336] (2)

1a	d3s86a_	A:
1b	d3s86b_	B:
1c	d3s86c_	C:
1d	d3s86d_	D:

(no "CATH Domain" information available for 3S86)

(no "Pfam Domain" information available for 3S86)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (IXTPA_THEMA | Q9WY06)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0017111	nucleoside-triphosphatase activity	Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
	GO:0047429	nucleoside-triphosphate diphosphatase activity	Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0009143	nucleoside triphosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
	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:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Phe A:79 - Pro A:80	[ RasMol ]
		Phe B:79 - Pro B:80	[ RasMol ]
		Phe C:79 - Pro C:80	[ RasMol ]
		Phe D:79 - Pro D:80	[ RasMol ]

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	3s86
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	3.6.1.15
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	IXTPA_THEMA \| Q9WY06	:	1vp2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Gene Ontology (8, 8)

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