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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE HUMAN LYMPHOID TYROSINE PHOSPHATASE CATALYTIC DOMAIN

Authors :   S. J. Tsai, U. Sen

Date :   14 Apr 09 (Deposition) - 02 Jun 09 (Release) - 07 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Sh2-Like Fold, Alternative Splicing, Cytoplasm, Hydrolase, Polymorphism, Protein Phosphatase, Systemic Lupus Erythematosus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Tsai, U. Sen, L. Zhao, W. B. Greenleaf, J. Dasgupta, E. Fiorillo, V. Orru, N. Bottini, X. S. Chen
Crystal Structure Of The Human Lymphoid Tyrosine Phosphatase Catalytic Domain: Insights Into Redox Regulation .
Biochemistry V. 48 4838 2009
PubMed-ID: 19371084 | Reference-DOI: 10.1021/BI900166Y
(for further references see the PDB file header)

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 22
	Chains	:	A
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A+
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	PTPN22, PTPN8
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE 70Z-PEP, LYMPHOID PHOSPHATASE, LYP

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	PO4	5	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:227 , SER A:228 , ALA A:229 , GLY A:230 , CYS A:231 , GLY A:232 , ARG A:233 , THR A:234 , GLN A:274 , HOH A:929	BINDING SITE FOR RESIDUE PO4 A 900
2	AC2	SOFTWARE	MET A:130 , GLU A:131 , TYR A:132 , HIS A:189 , LYS A:191 , HOH A:321	BINDING SITE FOR RESIDUE PO4 A 901
3	AC3	SOFTWARE	VAL A:48 , LYS A:51 , LYS A:53 , ASN A:54 , SER A:82 , SER A:83 , HOH A:931	BINDING SITE FOR RESIDUE PO4 A 902
4	AC4	SOFTWARE	GLU A:131 , TYR A:132 , LYS A:137 , HOH A:314 , HOH A:923	BINDING SITE FOR RESIDUE PO4 A 903
5	AC5	SOFTWARE	ARG A:233 , GLN A:278 , HOH A:338 , HOH A:987 , HOH A:1107	BINDING SITE FOR RESIDUE PO4 A 904

Asymmetric/Biological Unit

No.	Residues
1	A:129	-	A:227

(no "Cis Peptide Bond" information available for 3H2X)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_072629	S	201	F	PTN22_HUMAN	Polymorphism	7416347	A	S	201	F
2	UniProt	VAR_072630	R	263	Q	PTN22_HUMAN	Polymorphism	33996649	A	R	263	Q
3	UniProt	VAR_072631	R	266	W	PTN22_HUMAN	Polymorphism	72650670	A	R	266	W

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.	PTN22_HUMAN	24-289	1	A:24-289
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTN22_HUMAN	203-280	1	A:203-280
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTN22_HUMAN	225-235	1	A:225-235

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	ENST00000359785	1a	ENSE00001903805	chr1:114414381-114414159	223	PTN22_HUMAN	1-29	29	1	A:1-29	29
1.3	ENST00000359785	3	ENSE00002095549	chr1:114402082-114401974	109	PTN22_HUMAN	30-66	37	1	A:30-66	37
1.4b	ENST00000359785	4b	ENSE00002138335	chr1:114401700-114401624	77	PTN22_HUMAN	66-91	26	1	A:66-91	26
1.5	ENST00000359785	5	ENSE00002111906	chr1:114401195-114401100	96	PTN22_HUMAN	92-123	32	1	A:92-123	32
1.6	ENST00000359785	6	ENSE00002119544	chr1:114400398-114400360	39	PTN22_HUMAN	124-136	13	1	A:124-136	13
1.8	ENST00000359785	8	ENSE00002111803	chr1:114399241-114399170	72	PTN22_HUMAN	137-160	24	1	A:137-160	24
1.9	ENST00000359785	9	ENSE00002112169	chr1:114399063-114399004	60	PTN22_HUMAN	161-180	20	1	A:161-180	20
1.10	ENST00000359785	10	ENSE00002094492	chr1:114397671-114397529	143	PTN22_HUMAN	181-228	48	1	A:181-228	48
1.11	ENST00000359785	11	ENSE00002090732	chr1:114397159-114397093	67	PTN22_HUMAN	228-250	23	1	A:228-250	23
1.12	ENST00000359785	12	ENSE00002116075	chr1:114394726-114394649	78	PTN22_HUMAN	251-276	26	1	A:251-276	26
1.13	ENST00000359785	13	ENSE00002137845	chr1:114391248-114391162	87	PTN22_HUMAN	277-305	29	1	A:277-302	26
1.14	ENST00000359785	14	ENSE00002130300	chr1:114381242-114381166	77	PTN22_HUMAN	306-331	26	0	-	-
1.15	ENST00000359785	15	ENSE00002120084	chr1:114381029-114380212	818	PTN22_HUMAN	331-604	274	0	-	-
1.16	ENST00000359785	16	ENSE00002111199	chr1:114377615-114377532	84	PTN22_HUMAN	604-632	29	0	-	-
1.17	ENST00000359785	17	ENSE00002137375	chr1:114377061-114376931	131	PTN22_HUMAN	632-675	44	0	-	-
1.18a	ENST00000359785	18a	ENSE00000913528	chr1:114375760-114375733	28	PTN22_HUMAN	676-685	10	0	-	-
1.19	ENST00000359785	19	ENSE00000913529	chr1:114372651-114372571	81	PTN22_HUMAN	685-712	28	0	-	-
1.20	ENST00000359785	20	ENSE00000913530	chr1:114372329-114372214	116	PTN22_HUMAN	712-750	39	0	-	-
1.21	ENST00000359785	21	ENSE00001020762	chr1:114367794-114367764	31	PTN22_HUMAN	751-761	11	0	-	-
1.22b	ENST00000359785	22b	ENSE00001771523	chr1:114362276-114362199	78	PTN22_HUMAN	761-787	27	0	-	-
1.23d	ENST00000359785	23d	ENSE00001950193	chr1:114357591-114356433	1159	PTN22_HUMAN	787-807	21	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
	(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:302
 aligned with PTN22_HUMAN | Q9Y2R2 from UniProtKB/Swiss-Prot  Length:807

    Alignment length:302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
          PTN22_HUMAN     1 MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFIKGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSCEAEKRKSDYIIRTLKVKFNSETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPENFSVFSLIREMRTQRPSLVQTQEQYELVYNAVLELFKRQMDVIRDKHS 302
               SCOP domains d3h2xa_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........hhhhhh..hhhhh.......hhhhh................eeee........eeee......hhhhhhhhhhhh...eeee....ee..ee.............eee..eeeeeeeeee...eeeeeeeee....eeeeeeeee.......hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F-------------------------------------------------------------Q--W------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------TYR_PHOSPHATASE_PTP  PDB: A:24-289 UniProt: 24-289                                                                                                                                                                                                                        ------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:203-280 UniProt: 203-280                            ---------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1a  PDB: A:1-29       Exon 1.3  PDB: A:30-66 UniProt: 30-66-------------------------Exon 1.5  PDB: A:92-123         Exon 1.6     Exon 1.8  PDB: A:137-160Exon 1.9            Exon 1.10  PDB: A:181-228 UniProt: 181-228      ----------------------Exon 1.12  PDB: A:251-276 Exon 1.13  PDB: A:277-302  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.4b  PDB: A:66-91   ----------------------------------------------------------------------------------------------------------------------------------------Exon 1.11              ---------------------------------------------------- Transcript 1 (2)
                 3h2x A   1 MDQREILQKFLDEAQSKKITKEEFANEFLKLKRQSTKYKADKTYPTTVAEKPKNIKKNRYKDILPYDYSRVELSLITSDEDSSYINANFIKGVYGPKAYIATQGPLSTTLLDFWRMIWEYSVLIIVMACMEYEMGKKKCERYWAEPGEMQLEFGPFSVSCEAEKRKSDYIIRTLKVKFNSETRTIYQFHYKNWPDHDVPSSIDPILELIWDVRCYQEDDSVPICIHCSAGCGRTGVICAIDYTWMLLKDGIIPENFSVFSLIREMRTQRPSLVQTQEQYELVYNAVLELFKRQMDVIRDKHS 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

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Folds(

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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)

d3h2xa_

(no "CATH Domain" information available for 3H2X)

(no "Pfam Domain" information available for 3H2X)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PTN22_HUMAN | Q9Y2R2)

molecular function
	GO:0017124	SH3 domain binding	Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
	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:0019900	kinase binding	Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
	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.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0071225	cellular response to muramyl dipeptide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a muramyl dipeptide stimulus. Muramyl dipeptide is derived from peptidoglycan.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0031663	lipopolysaccharide-mediated signaling pathway	A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
	GO:0043508	negative regulation of JUN kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of JUN kinase activity.
	GO:0050868	negative regulation of T cell activation	Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation.
	GO:0050860	negative regulation of T cell receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0010507	negative regulation of autophagy	Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:1900165	negative regulation of interleukin-6 secretion	Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-6 secretion.
	GO:2000483	negative regulation of interleukin-8 secretion	Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-8 secretion.
	GO:0070433	negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway	Any process that stops, prevents, or reduces the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 2 (NOD2) pathway.
	GO:1903753	negative regulation of p38MAPK cascade	Any process that stops, prevents or reduces the frequency, rate or extent of p38MAPK cascade.
	GO:0032720	negative regulation of tumor necrosis factor production	Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0035644	phosphoanandamide dephosphorylation	The process of removing one or more phosphate groups from a phosphorylated anandamide.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:1902715	positive regulation of interferon-gamma secretion	Any process that activates or increases the frequency, rate or extent of interferon-gamma secretion.
	GO:1902523	positive regulation of protein K63-linked ubiquitination	Any process that activates or increases the frequency, rate or extent of protein K63-linked ubiquitination.
	GO:0034141	positive regulation of toll-like receptor 3 signaling pathway	Any process that activates or increases the frequency, rate, or extent of toll-like receptor 3 signaling pathway.
	GO:0034145	positive regulation of toll-like receptor 4 signaling pathway	Any process that activates or increases the frequency, rate, or extent of toll-like receptor 4 signaling pathway.
	GO:0032481	positive regulation of type I interferon production	Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0050855	regulation of B cell receptor signaling pathway	Any process that modulates the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a B cell.
	GO:1901222	regulation of NIK/NF-kappaB signaling	Any process that modulates the frequency, rate or extent of NIK/NF-kappaB signaling.
	GO:0050856	regulation of T cell receptor signaling pathway	Any process that modulates the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0045088	regulation of innate immune response	Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
	GO:0032817	regulation of natural killer cell proliferation	Any process that modulates the frequency, rate or extent of natural killer cell proliferation.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Asymmetric/Biological Unit
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	3h2x
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	PTN22_HUMAN \| Q9Y2R2
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	3.1.3.48
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	PTN22_HUMAN \| Q9Y2R2	:	2p6x 2qcj 2qct 3brh 3olr 3omh 4j51

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

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