2H4V - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE HUMAN TYROSINE RECEPTOR PHOSPHATASE GAMMA

Authors :   E. Ugochukwu, A. Barr, S. Das, J. Eswaran, P. Savitsky, M. Sundstrom, A. C. Arrowsmith, J. Weigelt, J. Debreczeni, F. Von Delft, S. Knapp, Str Genomics Consortium (Sgc)

Date :   25 May 06 (Deposition) - 11 Jul 06 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Tyrosine Receptor Phosphatase, Gamma, 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

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE GAMMA
	Chains	:	A, B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21 (DE3)-R3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PTPRG (RESIDUES 831-1127)
	Gene	:	PTPRG
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN-TYROSINE PHOSPHATASE GAMMA, R-PTP-GAMMA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 16)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	7	Ligand/Ion	CHLORIDE ION
3	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
4	FLC	1	Ligand/Ion	CITRATE ANION
5	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
4	FLC	1	Ligand/Ion	CITRATE ANION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	FLC	-1	Ligand/Ion	CITRATE ANION
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:131 , HOH A:621 , SER A:1046 , ARG A:1049 , ASP A:1074	BINDING SITE FOR RESIDUE CL A 801
02	AC2	SOFTWARE	ARG A:879 , TYR A:880 , ARG A:959 , ALA B:860	BINDING SITE FOR RESIDUE CL A 803
03	AC3	SOFTWARE	HOH A:229 , ASP B:887	BINDING SITE FOR RESIDUE CL B 804
04	AC4	SOFTWARE	HOH A:81 , HOH A:612 , LYS A:877 , ILE A:907 , ASN A:908 , GLN A:925	BINDING SITE FOR RESIDUE CL A 805
05	AC5	SOFTWARE	ASP A:887 , HIS A:888 , LYS A:892 , ALA A:987	BINDING SITE FOR RESIDUE CL A 806
06	AC6	SOFTWARE	GLN B:1104	BINDING SITE FOR RESIDUE CL B 1128
07	AC7	SOFTWARE	GLN B:856 , ARG B:1096 , GLN B:1104	BINDING SITE FOR RESIDUE CL B 1129
08	AC8	SOFTWARE	HOH B:52 , TYR B:1023 , THR B:1024 , GLN B:1025 , TRP B:1026	BINDING SITE FOR RESIDUE NA B 1130
09	AC9	SOFTWARE	HOH A:184 , HOH A:193 , HOH A:221 , HOH A:362 , HIS A:986 , TYR A:989 , VAL A:991 , ARG A:993 , HOH B:669 , EDO B:705 , LYS B:981 , ARG B:993	BINDING SITE FOR RESIDUE FLC A 1128
10	BC1	SOFTWARE	HOH A:36 , HOH A:75 , HOH A:616 , TYR A:880 , SER A:1061 , ALA A:1062 , ASN B:863 , ACT B:1131	BINDING SITE FOR RESIDUE ACT A 1129
11	BC2	SOFTWARE	ARG A:958 , ACT A:1129 , HOH B:180 , HOH B:658 , HOH B:659 , MET B:862 , ASN B:863 , ILE B:864	BINDING SITE FOR RESIDUE ACT B 1131
12	BC3	SOFTWARE	HOH B:352 , GLY B:914 , TYR B:915 , LYS B:917 , ALA B:920 , TYR B:921 , ARG B:1049 , SER B:1075 , GLN B:1078	BINDING SITE FOR RESIDUE EDO B 701
13	BC4	SOFTWARE	HOH A:42 , EDO A:703 , GLN A:856 , ARG A:1096 , TYR A:1101 , GLN A:1104	BINDING SITE FOR RESIDUE EDO A 702
14	BC5	SOFTWARE	HOH A:360 , EDO A:702 , ASN A:882 , GLN A:1104 , HOH B:501 , ASN B:863	BINDING SITE FOR RESIDUE EDO A 703
15	BC6	SOFTWARE	HOH A:642 , GLY A:914 , TYR A:915 , ALA A:920 , TYR A:921 , ARG A:1049 , SER A:1075 , GLN A:1078	BINDING SITE FOR RESIDUE EDO A 704
16	BC7	SOFTWARE	HOH A:313 , SER A:982 , THR A:983 , VAL A:991 , FLC A:1128 , HOH B:669 , SER B:982 , ARG B:993	BINDING SITE FOR RESIDUE EDO B 705

(no "SS Bond" information available for 2H4V)

(no "Cis Peptide Bond" information available for 2H4V)

(no "SAP(SNP)/Variant" information available for 2H4V)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTPRG_HUMAN	848-1119 1150-1410	2	A:848-1119 B:848-1119 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRG_HUMAN	1036-1110 1327-1401	2	A:1036-1110 B:1036-1110 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRG_HUMAN	1058-1068	2	A:1058-1068 B:1058-1068

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTPRG_HUMAN	848-1119 1150-1410	1	A:848-1119 - -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRG_HUMAN	1036-1110 1327-1401	1	A:1036-1110 - -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRG_HUMAN	1058-1068	1	A:1058-1068 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTPRG_HUMAN	848-1119 1150-1410	1	- B:848-1119 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRG_HUMAN	1036-1110 1327-1401	1	- B:1036-1110 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRG_HUMAN	1058-1068	1	- B:1058-1068

(no "Exon" information available for 2H4V)

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:278
 aligned with PTPRG_HUMAN | P23470 from UniProtKB/Swiss-Prot  Length:1445

    Alignment length:329
                                   803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113         
         PTPRG_HUMAN    794 CFQTAHFYVEDSSSPRVVPNESIPIIPIPDDMEAIPVKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTKVKKGQKGNPKGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1122
               SCOP domains d2h4                                va_ A: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2h4v                                A00 A:826-1122 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh--------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.......hhh.eee.....-----...eeeeeee........eeee...hhhhhhhhhhhhhhhh..eeee....ee..ee..........eeee..eeeeeeeeee...eeeeeeeeee..--------------.eeeeeeee...........hhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------TYR_PHOSPHATASE_PTP  PDB: A:848-1119 UniProt: 848-1119                                                                                                                                                                                                                          --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1036-1110 UniProt: 1036-1110                     ------------ PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------ PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2h4v A  826 YFQS--------------------------------MKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLP-----HSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK--------------ERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1122
                               |     -         -         -      |833       843       853       863       873       883       893   |   903       913       923       933       943       953       963       973       983       993      |  -         - |    1023      1033      1043      1053      1063      1073      1083      1093      1103      1113         
                             829                              830                                                                897   903                                                                                             1000           1015

Chain B from PDB  Type:PROTEIN  Length:280
 aligned with PTPRG_HUMAN | P23470 from UniProtKB/Swiss-Prot  Length:1445

    Alignment length:295
                                   837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117     
         PTPRG_HUMAN    828 IPVKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTKVKKGQKGNPKGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1122
               SCOP domains d2h4vb_ B: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2h4vB00 B:828-1122 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhh...........eee.....---hhhh.eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh..eeee....ee..ee..........eeee..eeeeeeeeee...eeeeeeeeee...------------.eeeeeeeee...........hhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------TYR_PHOSPHATASE_PTP  PDB: B:848-1119 UniProt: 848-1119                                                                                                                                                                                                                          --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:1036-1110 UniProt: 1036-1110                     ------------ PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2h4v B  828 QSMKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLP---SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTKV------------NERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1122
                                   837       847       857       867       877       887       897   |   907       917       927       937       947       957       967       977       987       997   |     -      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117     
                                                                                               897 901                                                                                                1001         1014

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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 Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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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)

1a	d2h4va_	A:
1b	d2h4vb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Protein-Tyrosine Phosphatase; Chain A (262)

Homologous Superfamily: Protein tyrosine phosphatase superfamily (228)

Human (Homo sapiens) (196)

1a	2h4vA00	A:826-1122
1b	2h4vB00	B:828-1122

(no "Pfam Domain" information available for 2H4V)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTPRG_HUMAN | P23470)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0005001	transmembrane receptor protein tyrosine phosphatase activity	Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by 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:0010633	negative regulation of epithelial cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
	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.
	GO:1903385	regulation of homophilic cell adhesion	Any process that modulates the frequency, rate or extent of homophilic cell adhesion.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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2fh7	CRYSTAL STRUCTURE OF THE PHOSPHATASE DOMAINS OF HUMAN PTP SIGMA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (17, 17)

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