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

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN INOSINE TRIPHOSPHATASE

Authors :   P. Stenmark, P. Kursula, C. Arrowsmith, H. Berglund, A. Edwards, M. Ehn, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, B. M. Hallberg, M. Hogbom, L. Holmberg Schiavone, T. Kotenyova, P. Nilsson-Ehle, T. Nyman, D. Ogg, C. Persson, J. Sagemark, H. Schuler, M. Sundstrom, A. G. Thorsell, S. Van Den Berg, J. Weigelt, P. Nordlund

Date :   22 Dec 05 (Deposition) - 04 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.09

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

Keywords :   Hydrolase, Inosine Triphosphate Pyrophosphohydrolase, Inosine Triphosphatase Deficiency, Itp, Imp, Disease Mutation, Nucleotide Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Stenmark, P. Kursula, S. Flodin, S. Graslund, R. Landry, P. Nordlund, H. Schuler
Crystal Structure Of Human Inosine Triphosphatase. Substrate Binding And Implication Of The Inosine Triphosphatase Deficiency Mutation P32T.
J. Biol. Chem. V. 282 3182 2007
PubMed-ID: 17138556 | Reference-DOI: 10.1074/JBC.M609838200

Molecule 1 - INOSINE TRIPHOSPHATE PYROPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A-LIC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A-LIC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INOSINE TRIPHOSPHATASE, ITPASE, ONCOGENE PROTEIN HLC14-06-P

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2CAR)

(no "Site" information available for 2CAR)

(no "SS Bond" information available for 2CAR)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:-1	-	Ser A:0
2	Leu A:83	-	Pro A:84
3	Leu B:83	-	Pro B:84

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_015576	P	32	T	ITPA_HUMAN	Disease (ITPAD)	1127354	A/B	P	32	T
2	UniProt	VAR_075084	R	178	C	ITPA_HUMAN	Unclassified (EIEE35)	746930990	A/B	R	178	C

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2CAR)

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000380113	2a	ENSE00001483921	chr20:3190006-3190263	258	ITPA_HUMAN	1-22	22	2	A:1-22 B:1-22	22 22
1.3	ENST00000380113	3	ENSE00000858731	chr20:3193815-3193872	58	ITPA_HUMAN	23-42	20	2	A:23-42 B:23-42	20 20
1.4b	ENST00000380113	4b	ENSE00000858732	chr20:3193965-3194029	65	ITPA_HUMAN	42-63	22	2	A:42-63 B:42-63	22 22
1.5	ENST00000380113	5	ENSE00000858733	chr20:3194631-3194704	74	ITPA_HUMAN	64-88	25	2	A:64-88 B:64-88	25 25
1.6b	ENST00000380113	6b	ENSE00001269727	chr20:3195927-3195958	32	ITPA_HUMAN	88-99	12	2	A:88-99 B:88-99	12 12
1.7b	ENST00000380113	7b	ENSE00001269752	chr20:3199163-3199278	116	ITPA_HUMAN	99-137	39	2	A:99-137 B:99-137	39 39
1.8b	ENST00000380113	8b	ENSE00001269713	chr20:3202487-3202563	77	ITPA_HUMAN	138-163	26	2	A:138-163 B:138-163	26 26
1.9c	ENST00000380113	9c	ENSE00001852672	chr20:3204012-3204516	505	ITPA_HUMAN	163-194	32	2	A:163-194 B:163-194	32 32

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:196
 aligned with ITPA_HUMAN | Q9BY32 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:196
                              1                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      
           ITPA_HUMAN     - --MAASLVGKKIVFVTGNAKKLEEVVQILGDKFPCTLVAQKIDLPEYQGEPDEISIQKCQEAVRQVQGPVLVEDTCLCFNALGGLPGPYIKWFLEKLKPEGLHQLLAGFEDKSAYALCTFALSTGDPSQPVRLFRGRTSGRIVAPRGCQDFGWDPCFQPDGYEQTYAEMPKAEKNAVSHRFRALLELQEYFGSLAA 194
               SCOP domains --d2cara1 A:1-194 Inosine triphosphate pyrophosphatase, ITPase                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeee..hhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..ee.hhhhhhhhhhhhhhhhh.......eeeeeeeeeee........eeeeeeeeeee..........hhh.eee..........hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------T-------------------------------------------------------------------------------------------------------------------------------------------------C---------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.2a  PDB: A:1-22Exon 1.3            ---------------------Exon 1.5  PDB: A:64-88   ----------Exon 1.7b  PDB: A:99-137               Exon 1.8b  PDB: A:138-163 ------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.4b  PDB: A:42-6------------------------Exon 1.6b   ---------------------------------------------------------------Exon 1.9c  PDB: A:163-194        Transcript 1 (2)
                 2car A  -1 GSMAASLVGKKIVFVTGNAKKLEEVVQILGDKFPCTLVAQKIDLPEYQGEPDEISIQKCQEAVRQVQGPVLVEDTCLCFNALGGLPGPYIKWFLEKLKPEGLHQLLAGFEDKSAYALCTFALSTGDPSQPVRLFRGRTSGRIVAPRGCQDFGWDPCFQPDGYEQTYAEMPKAEKNAVSHRFRALLELQEYFGSLAA 194
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188

Chain B from PDB  Type:PROTEIN  Length:194
 aligned with ITPA_HUMAN | Q9BY32 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           ITPA_HUMAN     1 MAASLVGKKIVFVTGNAKKLEEVVQILGDKFPCTLVAQKIDLPEYQGEPDEISIQKCQEAVRQVQGPVLVEDTCLCFNALGGLPGPYIKWFLEKLKPEGLHQLLAGFEDKSAYALCTFALSTGDPSQPVRLFRGRTSGRIVAPRGCQDFGWDPCFQPDGYEQTYAEMPKAEKNAVSHRFRALLELQEYFGSLAA 194
               SCOP domains d2carb_ B: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeeee..hhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh..ee.hhhhhhhhhhhhhhhhh.......eeeeeeeeeee........eeeeeeeeeee..........hhh.eee..........hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------T-------------------------------------------------------------------------------------------------------------------------------------------------C---------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:1-22Exon 1.3            ---------------------Exon 1.5  PDB: B:64-88   ----------Exon 1.7b  PDB: B:99-137               Exon 1.8b  PDB: B:138-163 ------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.4b  PDB: B:42-6------------------------Exon 1.6b   ---------------------------------------------------------------Exon 1.9c  PDB: B:163-194        Transcript 1 (2)
                 2car B   1 MAASLVGKKIVFVTGNAKKLEEVVQILGDKFPCTLVAQKIDLPEYQGEPDEISIQKCQEAVRQVQGPVLVEDTCLCFNALGGLPGPYIKWFLEKLKPEGLHQLLAGFEDKSAYALCTFALSTGDPSQPVRLFRGRTSGRIVAPRGCQDFGWDPCFQPDGYEQTYAEMPKAEKNAVSHRFRALLELQEYFGSLAA 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

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: automated matches (13)

Protein domain: automated matches (13)

Human (Homo sapiens) [TaxId: 9606] (5)

d2carb_

Family: ITPase (Ham1) (12)

Protein domain: Inosine triphosphate pyrophosphatase, ITPase (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2cara1

A:1-194

(no "CATH Domain" information available for 2CAR)

(no "Pfam Domain" information available for 2CAR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ITPA_HUMAN | Q9BY32)

molecular function
	GO:0036220	ITP diphosphatase activity	Catalysis of the reaction: ITP + H2O = IMP + diphosphate.
	GO:0036222	XTP diphosphatase activity	Catalysis of the reaction: XTP + H2O = xanthosine 5'-phosphate + diphosphate.
	GO:0035870	dITP diphosphatase activity	Catalysis of the reaction: dITP + H2O = dIMP + 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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0006193	ITP catabolic process	The chemical reactions and pathways resulting in the breakdown of ITP, inosine (5'-)triphosphate.
	GO:0051276	chromosome organization	A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
	GO:0009204	deoxyribonucleoside triphosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate on the sugar.
	GO:0055086	nucleobase-containing small molecule metabolic process	The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
	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).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2car)

	Sites
(no "Sites" information available for 2car)

	Cis Peptide Bonds
		Gly A:-1 - Ser A:0	[ RasMol ]
		Leu A:83 - Pro A:84	[ RasMol ]
		Leu B:83 - Pro B:84	[ RasMol ]

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	2car
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	ITPA_HUMAN \| Q9BY32
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	3.6.1.19
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	613850
		Disease Information	:	OMIM
	616647
		Disease Information	:	OMIM

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	ITPA_HUMAN \| Q9BY32
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	ITPA_HUMAN \| Q9BY32	:	2i5d 2j4e 4f95

(no "Related Entries Specified in the PDB File" available for 2CAR)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (0, 0)

Exons (8, 16)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (0, 0)

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Gene Ontology (15, 15)

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