2PA5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN9

Authors :   E. Ugochukwu, A. Barr, A. C. W. Pike, P. Savitsky, E. Papagrigoriou, A. T J. Uppenberg, G. Bunkoczi, E. Salah, S. Das, F. Von Delft, M. Sundstro C. H. Arrowsmith, J. Weigelt, A. Edwards, S. Knapp, Structural Genom Consortium (Sgc)

Date :   27 Mar 07 (Deposition) - 15 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Protein Tyrosine Phosphatase, Meg2, Ptpn9, 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 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 9
	Chains	:	A, B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-CH
	Expression System Strain	:	PHAGE-RESISTANT DERIVATIVE OF BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PTPN9
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN-TYROSINE PHOSPHATASE MEG2, PTPASE-MEG2

		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 (3, 10)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
3	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	SCN	1	Ligand/Ion	THIOCYANATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	SCN	-1	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:402 , LYS A:411 , SER A:516 , HOH A:761	BINDING SITE FOR RESIDUE CL A 591
2	AC2	SOFTWARE	ARG B:332 , ARG B:410 , HOH B:764	BINDING SITE FOR RESIDUE CL B 590
3	AC3	SOFTWARE	ARG A:332	BINDING SITE FOR RESIDUE CL A 592
4	AC4	SOFTWARE	ALA A:478 , ILE A:481 , PHE A:574 , LYS A:577 , HOH A:750 , HOH A:919	BINDING SITE FOR RESIDUE SCN A 601
5	AC5	SOFTWARE	SER A:475 , ASP B:335 , ALA B:517 , GLN B:559 , HOH B:733	BINDING SITE FOR RESIDUE EDO B 701
6	AC6	SOFTWARE	GLY B:365 , TYR B:366 , GLN B:368 , ALA B:371 , TYR B:372 , ASP B:529 , ILE B:530	BINDING SITE FOR RESIDUE EDO B 702
7	AC7	SOFTWARE	GLN A:289 , ARG A:425 , GLY A:427 , MET A:580 , VAL A:581 , SER A:582 , HOH A:921	BINDING SITE FOR RESIDUE EDO A 703
8	AC8	SOFTWARE	PRO A:474 , SER A:475 , PHE A:566 , LYS A:569 , ALA A:570 , GLU A:573 , HOH A:809 , HOH A:845	BINDING SITE FOR RESIDUE EDO A 704
9	AC9	SOFTWARE	LEU A:466 , ARG B:312 , HOH B:771 , HOH B:786 , HOH B:823	BINDING SITE FOR RESIDUE EDO B 705

(no "SS Bond" information available for 2PA5)

Asymmetric Unit

No.	Residues
1	Gly A:282	-	Pro A:283

(no "SAP(SNP)/Variant" information available for 2PA5)

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.	PTN9_HUMAN	303-574	2	A:303-574 B:303-574
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTN9_HUMAN	481-565	2	A:481-565 B:481-565
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTN9_HUMAN	513-523	2	A:513-523 B:513-523

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.	PTN9_HUMAN	303-574	1	A:303-574 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTN9_HUMAN	481-565	1	A:481-565 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTN9_HUMAN	513-523	1	A:513-523 -

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.	PTN9_HUMAN	303-574	1	- B:303-574
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTN9_HUMAN	481-565	1	- B:481-565
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTN9_HUMAN	513-523	1	- B:513-523

(no "Exon" information available for 2PA5)

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:296
 aligned with PTN9_HUMAN | P43378 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:308
                                   286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576        
           PTN9_HUMAN   277 SVHVPGPHAMTIQELVDYVNARQKQGIYEEYEDIRRENPVGTFHCSMSPGNLEKNRYGDVPCLDQTRVKLTKRSGHTQTDYINASFMDGYKQKNAYIGTQGPLENTYRDFWLMVWEQKVLVIVMTTRFEEGGRRKCGQYWPLEKDSRIRFGFLTVTNLGVENMNHYKKTTLEIHNTEERQKRQVTHFQFLSWPDYGVPSSAASLIDFLRVVRNQQSLAVSNMGARSKGQCPEPPIVVHCSAGIGRTGTFCSLDICLAQLEELGTLNVFQTVSRMRTQRAFSIQTPEQYYFCYKAILEFAEKEGMVSSG 584
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pa5A00 A:277-584 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhh...........eee...-----...eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhh...eeee....ee..ee............eeee..eeeeeeeeee...eeeeeeeeee....eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.-------...eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------TYR_PHOSPHATASE_PTP  PDB: A:303-574 UniProt: 303-574                                                                                                                                                                                                                            ---------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:481-565 UniProt: 481-565                                   ------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pa5 A 277 SVHVPGPHAMTIQELVDYVNARQKQGIYEEYEDIRRENPVGTFHCSMSPGNLEKNRYGDVPCLDQTRVKLTK-----QTDYINASFMDGYKQKNAYIGTQGPLENTYRDFWLMVWEQKVLVIVMTTRFEEGGRRKCGQYWPLEKDSRIRFGFLTVTNLGVENMNHYKKTTLEIHNTEERQKRQVTHFQFLSWPDYGVPSSAASLIDFLRVVRNQQSLAVSNMGA-------EPPIVVHCSAGIGRTGTFCSLDICLAQLEELGTLNVFQTVSRMRTQRAFSIQTPEQYYFCYKAILEFAEKEGMVSAH 584
                                   286       296       306       316       326       336       346 |     356       366       376       386       396       406       416       426       436       446       456       466       476       486       496   |     - |     516       526       536       546       556       566       576        
                                                                                                 348   354                                                                                                                                               500     508

Chain B from PDB  Type:PROTEIN  Length:291
 aligned with PTN9_HUMAN | P43378 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:305
                                   286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576     
           PTN9_HUMAN   277 SVHVPGPHAMTIQELVDYVNARQKQGIYEEYEDIRRENPVGTFHCSMSPGNLEKNRYGDVPCLDQTRVKLTKRSGHTQTDYINASFMDGYKQKNAYIGTQGPLENTYRDFWLMVWEQKVLVIVMTTRFEEGGRRKCGQYWPLEKDSRIRFGFLTVTNLGVENMNHYKKTTLEIHNTEERQKRQVTHFQFLSWPDYGVPSSAASLIDFLRVVRNQQSLAVSNMGARSKGQCPEPPIVVHCSAGIGRTGTFCSLDICLAQLEELGTLNVFQTVSRMRTQRAFSIQTPEQYYFCYKAILEFAEKEGMV 581
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pa5B0 0 B:277-581 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) ------ -------------------------------------------Y_phosphatase-2pa5B01 B:327-573                                                                                                                                                                                                                        -------- Pfam domains (1)
           Pfam domains (2) ------ -------------------------------------------Y_phosphatase-2pa5B02 B:327-573                                                                                                                                                                                                                        -------- Pfam domains (2)
         Sec.struct. author ......-...hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhh.......hhh.eee...........eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhh...eeee....ee..ee............eeee..eeeeeeeeee...eeeeeeeeee....eeeeeeeeee...-----...hhhhhhhhhhhhhhhhhhhhhh--------....eeeee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------TYR_PHOSPHATASE_PTP  PDB: B:303-574 UniProt: 303-574                                                                                                                                                                                                                            ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:481-565 UniProt: 481-565                                   ---------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA---------------------------------------------------------- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pa5 B 277 SVHVPG-HAMTIQELVDYVNARQKQGIYEEYEDIRRENPVGTFHCSMSPGNLEKNRYGDVPCLDQTRVKLTKRSGHTQTDYINASFMDGYKQKNAYIGTQGPLENTYRDFWLMVWEQKVLVIVMTTRFEEGGRRKCGQYWPLEKDSRIRFGFLTVTNLGVENMNHYKKTTLEIHNTEERQKRQVTHFQFLSW-----PSSAASLIDFLRVVRNQQSLAVSNM--------PEPPIVVHCSAGIGRTGTFCSLDICLAQLEELGTLNVFQTVSRMRTQRAFSIQTPEQYYFCYKAILEFAEKEGMV 581
                                 | 286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466 |     476       486       496 |       -|      516       526       536       546       556       566       576     
                               282 |                                                                                                                                                                                     468   474                     498      507                                                                          
                                 284

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 '\|'

(no "SCOP Domain" information available for 2PA5)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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	2pa5B00	B:277-581
1b	2pa5A00	A:277-584

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: Y_phosphatase (93)

Homo sapiens (Human) (82)

1a	Y_phosphatase-2pa5B01	B:327-573
1b	Y_phosphatase-2pa5B02	B:327-573

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTN9_HUMAN | P43378)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:282 - Pro A:283	[ RasMol ]

Biological Units
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	2pa5
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	PTN9_HUMAN \| P43378
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	3.1.3.48
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	PTN9_HUMAN \| P43378	:	4ge2 4ge5 4ge6 4icz

2hnq	CRYSTAL STRUCTURE OF HUMAN PROTEIN TYROSINE PHOSPHATASE 1B

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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