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Title :   CRYSTAL STRUCTURE OF A C-TERMINAL PHOSPHATASE DOMAIN OF RATTUS NORVEGICUS ORTHOLOG OF HUMAN PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, D (PTPRD)

Authors :   J. B. Bonanno, J. Gilmore, K. T. Bain, M. Iizuka, W. Xu, S. Wasserman, D. S J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)

Date :   10 Nov 06 (Deposition) - 21 Nov 06 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Phosphatase, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Almo, J. B. Bonanno, J. M. Sauder, S. Emtage, T. P. Dilorenzo, V. Malashkevich, S. R. Wasserman, S. Swaminathan, S. Eswaramoorthy, R. Agarwal, D. Kumaran, M. Madegowda, S. Ragumani, Y. Patskovsky, J. Alvarado, U. A. Ramagopal, J. Faber-Barata, M. R. Chance, A. Sali, A. Fiser, Z. Y. Zhang, D. S. Lawrence, S. K. Burley
Structural Genomics Of Protein Phosphatases.
J. Struct. Funct. Genom. V. 8 121 2007
PubMed-ID: 18058037 | Reference-DOI: 10.1007/S10969-007-9036-1

Molecule 1 - PTPRD, PHOSPHATASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	MODIFIED PET26
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PTPRD
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2NV5)

(no "Site" information available for 2NV5)

(no "SS Bond" information available for 2NV5)

(no "Cis Peptide Bond" information available for 2NV5)

(no "SAP(SNP)/Variant" information available for 2NV5)

Asymmetric Unit (3, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTPRS_RAT	1352-1607 1639-1898	3	A:1229-1483 B:1229-1483 C:1229-1483 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRS_RAT	1527-1598 1816-1889	3	A:1403-1473 B:1403-1473 C:1403-1473 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRS_RAT	1546-1556 1837-1847	3	A:1422-1432 B:1422-1432 C:1422-1432 -

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.	PTPRS_RAT	1352-1607 1639-1898	1	A:1229-1483 - - -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRS_RAT	1527-1598 1816-1889	1	A:1403-1473 - - -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRS_RAT	1546-1556 1837-1847	1	A:1422-1432 - - -

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.	PTPRS_RAT	1352-1607 1639-1898	1	- B:1229-1483 - -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRS_RAT	1527-1598 1816-1889	1	- B:1403-1473 - -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRS_RAT	1546-1556 1837-1847	1	- B:1422-1432 - -

Biological Unit 3 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTPRS_RAT	1352-1607 1639-1898	1	- - C:1229-1483 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPRS_RAT	1527-1598 1816-1889	1	- - C:1403-1473 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPRS_RAT	1546-1556 1837-1847	1	- - C:1422-1432 -

(no "Exon" information available for 2NV5)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:283
 aligned with PTPRS_RAT | Q64605 from UniProtKB/Swiss-Prot  Length:1907

    Alignment length:283
                                  1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607   
           PTPRS_RAT   1328 SHPPIPITDMAEHMERLKANDSLKLSQEYESIDPGQQFTWEHSNLEANKPKNRYANVIAYDHSRVILQPLEGIMGSDYINANYVDGYRRQNAYIATQGPLPETFGDFWRMVWEQRSATVVMMTRLEEKSRVKCDQYWPNRGTETYGFIQVTLLDTMELATFCVRTFSLHKNGSSEKREVRHFQFTAWPDHGVPEYPTPFLAFLRRVKTCNPPDAGPVVVHCSAGVGRTGCFIVIDAMLERIRTEKTVDVYGHVTLMRSQRNYMVQTEDQYSFIHEALLEAVGC 1610
               SCOP domains d2nv5a_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2nv5A00 A:1204-1486 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhh.......hhh.eee...........eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhh...eeee....ee..ee..........eeee..eeeeeeeeee...eeeeeeeeee......eeeeeeee...........hhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhheehhhhhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------TYR_PHOSPHATASE_PTP  PDB: A:1229-1483 UniProt: 1352-1607                                                                                                                                                                                                        --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1403-1473 UniProt: 1527-1598                  ------------ PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2nv5 A 1204 SHPPIPILELADHIERLKANDNLKFSQEYESIDPGQQFTWEHSNLEVNKPKNRYANVIAYDHSRVLLSAIEGIPGSDYVNANYIDGYRKQNAYIATQGSLPETFGDFWRMIWEQRSATVVMMTKLEERSRVKCDQYWPSRGTETHGLVQVTLLDTVELATYCVRTFALYKNGSSEKREVRQFQFTAWPDHGVPEHPTPFLAFLRRVKTCNPPDAGPMVVHCSAGVGRTGCFIVIDAMLERIKHEKTVDIYGHVTLMRAQRNYMVQTEDQYIFIHDALLEAVTC 1486
                                  1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with PTPRS_RAT | Q64605 from UniProtKB/Swiss-Prot  Length:1907

    Alignment length:283
                                  1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607   
           PTPRS_RAT   1328 SHPPIPITDMAEHMERLKANDSLKLSQEYESIDPGQQFTWEHSNLEANKPKNRYANVIAYDHSRVILQPLEGIMGSDYINANYVDGYRRQNAYIATQGPLPETFGDFWRMVWEQRSATVVMMTRLEEKSRVKCDQYWPNRGTETYGFIQVTLLDTMELATFCVRTFSLHKNGSSEKREVRHFQFTAWPDHGVPEYPTPFLAFLRRVKTCNPPDAGPVVVHCSAGVGRTGCFIVIDAMLERIRTEKTVDVYGHVTLMRSQRNYMVQTEDQYSFIHEALLEAVGC 1610
               SCOP domains d2nv5b_ B: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2nv5B00 B:1204-1486 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..hhhhhhhhhhhhhhhhhhhhhhh........hhhhhh..hhhhh...........eee...........eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh..eeee....................eeee..eeeeeeeeee...eeeeeeeeee.....eeeeeeeee...........hhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------TYR_PHOSPHATASE_PTP  PDB: B:1229-1483 UniProt: 1352-1607                                                                                                                                                                                                        --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:1403-1473 UniProt: 1527-1598                  ------------ PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2nv5 B 1204 SHPPIPILELADHIERLKANDNLKFSQEYESIDPGQQFTWEHSNLEVNKPKNRYANVIAYDHSRVLLSAIEGIPGSDYVNANYIDGYRKQNAYIATQGSLPETFGDFWRMIWEQRSATVVMMTKLEERSRVKCDQYWPSRGTETHGLVQVTLLDTVELATYCVRTFALYKNGSSEKREVRQFQFTAWPDHGVPEHPTPFLAFLRRVKTCNPPDAGPMVVHCSAGVGRTGCFIVIDAMLERIKHEKTVDIYGHVTLMRAQRNYMVQTEDQYIFIHDALLEAVTC 1486
                                  1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483

Chain C from PDB  Type:PROTEIN  Length:283
 aligned with PTPRS_RAT | Q64605 from UniProtKB/Swiss-Prot  Length:1907

    Alignment length:283
                                  1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607   
           PTPRS_RAT   1328 SHPPIPITDMAEHMERLKANDSLKLSQEYESIDPGQQFTWEHSNLEANKPKNRYANVIAYDHSRVILQPLEGIMGSDYINANYVDGYRRQNAYIATQGPLPETFGDFWRMVWEQRSATVVMMTRLEEKSRVKCDQYWPNRGTETYGFIQVTLLDTMELATFCVRTFSLHKNGSSEKREVRHFQFTAWPDHGVPEYPTPFLAFLRRVKTCNPPDAGPVVVHCSAGVGRTGCFIVIDAMLERIRTEKTVDVYGHVTLMRSQRNYMVQTEDQYSFIHEALLEAVGC 1610
               SCOP domains d2nv5c_ C: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2nv5C00 C:1204-1486 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) -----------------------------------------------Y_phosphatase-2nv5C01 C:1251-1482                                                                                                                                                                                                       ---- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------Y_phosphatase-2nv5C02 C:1251-1482                                                                                                                                                                                                       ---- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------Y_phosphatase-2nv5C03 C:1251-1482                                                                                                                                                                                                       ---- Pfam domains (3)
         Sec.struct. author ....ee..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..hhhhh.......hhh.eee...........eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh..eeee....ee..ee..........eeee..eeeeeeeeee...eeeeeeeeee......eeeeeeee...........hhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhheehhhhhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------TYR_PHOSPHATASE_PTP  PDB: C:1229-1483 UniProt: 1352-1607                                                                                                                                                                                                        --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: C:1403-1473 UniProt: 1527-1598                  ------------ PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2nv5 C 1204 SHPPIPILELADHIERLKANDNLKFSQEYESIDPGQQFTWEHSNLEVNKPKNRYANVIAYDHSRVLLSAIEGIPGSDYVNANYIDGYRKQNAYIATQGSLPETFGDFWRMIWEQRSATVVMMTKLEERSRVKCDQYWPSRGTETHGLVQVTLLDTVELATYCVRTFALYKNGSSEKREVRQFQFTAWPDHGVPEHPTPFLAFLRRVKTCNPPDAGPMVVHCSAGVGRTGCFIVIDAMLERIKHEKTVDIYGHVTLMRAQRNYMVQTEDQYIFIHDALLEAVTC 1486
                                  1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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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)

Norway rat (Rattus norvegicus) [TaxId: 10116] (2)

1a	d2nv5a_	A:
1b	d2nv5b_	B:
1c	d2nv5c_	C:

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)

Norway rat (Rattus norvegicus) (4)

1a	2nv5A00	A:1204-1486
1b	2nv5B00	B:1204-1486
1c	2nv5C00	C:1204-1486

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: Y_phosphatase (93)

Rattus norvegicus (Rat) (1)

1a	Y_phosphatase-2nv5C01	C:1251-1482
1b	Y_phosphatase-2nv5C02	C:1251-1482
1c	Y_phosphatase-2nv5C03	C:1251-1482

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PTPRS_RAT | Q64605)

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: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:0004725	protein tyrosine phosphatase activity	Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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