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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN PROTEIN TYROSINE PHOSPHATASE NON-RECEPTOR TYPE 18

Authors :   E. Ugochukwu, A. Barr, I. Alfano, F. Gorrec, C. Umeano, P. Savitsky, F. Sobott, J. Eswaran, E. Papagrigoriou, J. E. Debreczeni, A. Turnbull, G. Bunkoczi, M. Sundstrom, C. H. Arrowsmith, J. Weigelt, A. Edwards, F. Von Delft, S. Knapp, Structural Genomics Consortium (Sgc)

Date :   20 Dec 06 (Deposition) - 30 Jan 07 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Protein Tyrosine Phosphatase, Receptor, Human, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Barr, E. Ugochukwu, W. H. Lee, O. N. King, P. Filippakopoulos, I. Alfano, P. Savitsky, N. A. Burgess-Brown, S. Muller, S. Knapp
Large-Scale Structural Analysis Of The Classical Human Protein Tyrosine Phosphatome.
Cell(Cambridge, Mass. ) V. 136 352 2009
PubMed-ID: 19167335 | Reference-DOI: 10.1016/J.CELL.2008.11.038
(for further references see the PDB file header)

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 18
	Chains	:	A
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P2
	Expression System Strain	:	BL21(DE3) PHAGE RESISTANT
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PTPN18
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BRAIN-DERIVED PHOSPHATASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2OC3)

(no "Site" information available for 2OC3)

(no "SS Bond" information available for 2OC3)

(no "Cis Peptide Bond" information available for 2OC3)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047651	M	193	V	PTN18_HUMAN	Polymorphism	3739124	A	M	193	V

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTN18_HUMAN	26-291	1	A:26-291
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTN18_HUMAN	205-282	1	A:205-282
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTN18_HUMAN	227-237	1	A:227-237

Asymmetric/Biological Unit (11, 11)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000175756	1a	ENSE00001776329	chr2:131113580-131113773	194	PTN18_HUMAN	1-31	31	1	A:6-31 (gaps)	26
1.3b	ENST00000175756	3b	ENSE00001793686	chr2:131116440-131116548	109	PTN18_HUMAN	32-68	37	1	A:32-68	37
1.4b	ENST00000175756	4b	ENSE00001668508	chr2:131116806-131116882	77	PTN18_HUMAN	68-93	26	1	A:68-93	26
1.5a	ENST00000175756	5a	ENSE00001650051	chr2:131116970-131117065	96	PTN18_HUMAN	94-125	32	1	A:94-125	32
1.5c	ENST00000175756	5c	ENSE00001657754	chr2:131117181-131117219	39	PTN18_HUMAN	126-138	13	1	A:126-138	13
1.7b	ENST00000175756	7b	ENSE00001790718	chr2:131126706-131126774	69	PTN18_HUMAN	139-161	23	1	A:139-161	23
1.8	ENST00000175756	8	ENSE00001673375	chr2:131127338-131127400	63	PTN18_HUMAN	162-182	21	1	A:162-182	21
1.9b	ENST00000175756	9b	ENSE00000776192	chr2:131127621-131127763	143	PTN18_HUMAN	183-230	48	1	A:183-230	48
1.9i	ENST00000175756	9i	ENSE00000776193	chr2:131128130-131128196	67	PTN18_HUMAN	230-252	23	1	A:230-252	23
1.9l	ENST00000175756	9l	ENSE00000776194	chr2:131128278-131128355	78	PTN18_HUMAN	253-278	26	1	A:253-278	26
1.9n	ENST00000175756	9n	ENSE00000776195	chr2:131128448-131128537	90	PTN18_HUMAN	279-308	30	1	A:279-293	15
1.10a	ENST00000175756	10a	ENSE00000776196	chr2:131128772-131128860	89	PTN18_HUMAN	309-338	30	0	-	-
1.11d	ENST00000175756	11d	ENSE00000776197	chr2:131129830-131130056	227	PTN18_HUMAN	338-414	77	0	-	-
1.12b	ENST00000175756	12b	ENSE00000857404	chr2:131130446-131130520	75	PTN18_HUMAN	414-439	26	0	-	-
1.13e	ENST00000175756	13e	ENSE00001159610	chr2:131130730-131132982	2253	PTN18_HUMAN	439-460	22	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:279
 aligned with PTN18_HUMAN | Q99952 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:288
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285        
          PTN18_HUMAN     6 DSARSFLERLEARGGREGAVLAGEFSDIQACSAAWKADGVCSTVAGSRPENVRKNRYKDVLPYDQTRVILSLLQEEGHSDYINGNFIRGVDGSLAYIATQGPLPHTLLDFWRLVWEFGVKVILMACREIENGRKRCERYWAQEQEPLQTGLFCITLIKEKWLNEDIMLRTLKVTFQKESRSVYQLQYMSWPDRGVPSSPDHMLAMVEEARRLQGSGPEPLCVHCSAGCGRTGVLCTVDYVRQLLLTQMIPPDFSLFDVVLKMRKQRPAAVQTEEQYRFLYHTVAQMFC 293
               SCOP domains d2o c3a_ A        : automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------Y_phosphatase-2oc3A01 A:56-290                                                                                                                                                                                                             --- Pfam domains
         Sec.struct. author ...-hhhhhh--------hhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhh.......hhh.eee...hhhhh...eeeeeeee.....eeeeee...hhhhhhhhhhhhhhh...eeee....ee..ee............eee..eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeee...........hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------TYR_PHOSPHATASE_PTP  PDB: A:26-291 UniProt: 26-291                                                                                                                                                                                                                        -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:205-282 UniProt: 205-282                            ----------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA-------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1a UniProt: 1-31   Exon 1.3b  PDB: A:32-68              -------------------------Exon 1.5a  PDB: A:94-125        Exon 1.5c    Exon 1.7b              Exon 1.8             Exon 1.9b  PDB: A:183-230 UniProt: 183-230      ----------------------Exon 1.9l  PDB: A:253-278 Exon 1.9n       Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.4b  PDB: A:68-93   ----------------------------------------------------------------------------------------------------------------------------------------Exon 1.9i              ----------------------------------------- Transcript 1 (2)
                 2oc3 A   6 DSA-SFLERL--------AVLAGEFSDIQACSAAWKADGVCSTVAGSRPENVRKNRYKDVLPYDQTRVILSLLQEEGHSDYINGNFIRGVDGSLAYIATQGPLPHTLLDFWRLVWEFGVKVILMACREIENGRKRCERYWAQEQEPLQTGLFCITLIKEKWLNEDIMLRTLKVTFQKESRSVYQLQYMSWPDRGVPSSPDHMLAMVEEARRLQGSGPEPLCVHCSAGCGRTGVLCTVDYVRQLLLTQMIPPDFSLFDVVLKMRKQRPAAVQTEEQYRFLYHTVAQMFC 293
                              | |   15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285        
                              8 |   15       24                                                                                                                                                                                                                                                                             
                               10

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: (Phosphotyrosine protein) phosphatases II (296)

Superfamily: (Phosphotyrosine protein) phosphatases II (296)

Family: automated matches (83)

Protein domain: automated matches (83)

Human (Homo sapiens) [TaxId: 9606] (76)

d2oc3a_

(no "CATH Domain" information available for 2OC3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: Y_phosphatase (93)

Homo sapiens (Human) (82)

Y_phosphatase-2oc3A01

A:56-290

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PTN18_HUMAN | Q99952)

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:0004726	non-membrane spanning protein tyrosine phosphatase activity	Catalysis of the reaction: non-membrane spanning protein tyrosine phosphate + H2O = non-membrane spanning protein tyrosine + phosphate.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004721	phosphoprotein phosphatase activity	Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004725	protein tyrosine phosphatase activity	Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	PTN18_HUMAN \| Q99952	:	4gfu 4gfv 4nnd

1gwz	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE PROTEIN TYROSINE PHOSPHATASE SHP-1
2b49	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 3

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