1FPR - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOMAIN OF SHP-1 AND AN IN VITRO PEPTIDE SUBSTRATE PY469 DERIVED FROM SHPS-1.

Authors :   J. Yang, Z. Cheng, Z. Niu, Z. J. Zhao, G. W. Zhou

Date :   31 Aug 00 (Deposition) - 07 Mar 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Protein Tyrosine Phosphatase, Substrate Specificity, Residue Shift, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Yang, Z. Cheng, T. Niu, X. Liang, Z. J. Zhao, G. W. Zhou
Structural Basis For Substrate Specificity Of Protein-Tyrosine Phosphatase Shp-1.
J. Biol. Chem. V. 275 4066 2000
PubMed-ID: 10660565 | Reference-DOI: 10.1074/JBC.275.6.4066
(for further references see the PDB file header)

Molecule 1 - PROTEIN-TYROSINE PHOSPHATASE 1C
	Chains	:	A
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PTP-1C, HEMATOPOIETIC CELL PROTEIN-TYROSINE PHOSPHATASE, SH-PTP1

Molecule 2 - PEPTIDE PY469
	Chains	:	B
	Engineered	:	YES
	Other Details	:	THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS)
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

(no "Site" information available for 1FPR)

Asymmetric Unit

No.	Residues
1	A:329	-	A:363

(no "Cis Peptide Bond" information available for 1FPR)

(no "SAP(SNP)/Variant" information available for 1FPR)

Asymmetric 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.	PTN6_HUMAN	244-515	1	A:246-517
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTN6_HUMAN	430-506	1	A:432-508
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTN6_HUMAN	451-461	1	A:453-463

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.	PTN6_HUMAN	244-515	1	A:246-517
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTN6_HUMAN	430-506	1	A:432-508
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTN6_HUMAN	451-461	1	A:453-463

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	PTN6_HUMAN	244-515	2	A:246-517
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTN6_HUMAN	430-506	2	A:432-508
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTN6_HUMAN	451-461	2	A:453-463

Asymmetric Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3	ENST00000318974	3	ENSE00001164365	chr12:7060434-7060683	250	PTN6_HUMAN	1-3	3	0	-	-
1.4	ENST00000318974	4	ENSE00000866991	chr12:7060772-7060894	123	PTN6_HUMAN	3-44	42	0	-	-
1.5	ENST00000318974	5	ENSE00000716206	chr12:7061146-7061340	195	PTN6_HUMAN	44-109	66	0	-	-
1.6	ENST00000318974	6	ENSE00000716209	chr12:7063968-7064157	190	PTN6_HUMAN	109-172	64	0	-	-
1.7	ENST00000318974	7	ENSE00000716212	chr12:7064314-7064430	117	PTN6_HUMAN	173-211	39	0	-	-
1.8	ENST00000318974	8	ENSE00000716214	chr12:7064535-7064648	114	PTN6_HUMAN	212-249	38	1	A:245-251	7
1.9	ENST00000318974	9	ENSE00000716216	chr12:7064823-7064919	97	PTN6_HUMAN	250-282	33	1	A:252-284	33
1.10	ENST00000318974	10	ENSE00000716218	chr12:7065305-7065384	80	PTN6_HUMAN	282-308	27	1	A:284-310	27
1.11	ENST00000318974	11	ENSE00000716220	chr12:7065582-7065731	150	PTN6_HUMAN	309-358	50	1	A:311-360	50
1.12	ENST00000318974	12	ENSE00000716222	chr12:7066817-7066948	132	PTN6_HUMAN	359-402	44	1	A:361-404	44
1.13	ENST00000318974	13	ENSE00000716225	chr12:7067082-7067236	155	PTN6_HUMAN	403-454	52	1	A:405-456	52
1.14	ENST00000318974	14	ENSE00000716227	chr12:7069090-7069157	68	PTN6_HUMAN	454-477	24	1	A:456-479	24
1.15	ENST00000318974	15	ENSE00000716229	chr12:7069251-7069402	152	PTN6_HUMAN	477-527	51	1	A:479-528	50
1.16	ENST00000318974	16	ENSE00000716231	chr12:7069507-7069598	92	PTN6_HUMAN	528-558	31	0	-	-
1.17c	ENST00000318974	17c	ENSE00001358823	chr12:7069969-7070108	140	PTN6_HUMAN	558-595	38	0	-	-
1.18	ENST00000318974	18	ENSE00001365384	chr12:7070289-7070479	191	PTN6_HUMAN	-	0	0	-	-

Asymmetric Unit

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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:284
 aligned with PTN6_HUMAN | P29350 from UniProtKB/Swiss-Prot  Length:595

    Alignment length:284
                                   252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522    
          PTN6_HUMAN    243 GFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYIKNQLLGPDENAKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHCSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEVL  526
               SCOP domains d1fpra_ A: Tyrosine phosphatase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1fprA00 A:245-528 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.................................eee............eeeee.ee....hhhhh..eee.....hhhhhhhhhhhhhhh...eeee....................eeeee..eeeeeeee........eeeeeee.......eeeee..............hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TYR_PHOSPHATASE_PTP  PDB: A:246-517 UniProt: 244-515                                                                                                                                                                                                                            ----------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:432-508 UniProt: 430-506                           -------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) 1.8    --------------------------------Exon 1.10  PDB: A:284-310  Exon 1.11  PDB: A:311-360 UniProt: 309-358        Exon 1.12  PDB: A:361-404 UniProt: 359-402  Exon 1.13  PDB: A:405-456 UniProt: 403-454          ----------------------Exon 1.15  PDB: A:479-528 UniProt: 477-527         Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.9  PDB: A:252-284         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:456-47------------------------------------------------- Transcript 1 (2)
                1fpr A  245 GFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYIKNQLLGPDENAKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHSSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEVL  528
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524

Chain B from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                1fpr B 1464 EDTLTyADLD 1473
                                 |1473
                              1469-PTR

Legend:		→ Mismatch	(orange background)
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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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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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)

1fprA00

A:245-528

(no "Pfam Domain" information available for 1FPR)

Asymmetric Unit(hide GO term definitions)

Chain A (PTN6_HUMAN | P29350)

molecular function
	GO:0042169	SH2 domain binding	Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
	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: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:0001784	phosphotyrosine residue binding	Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	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:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0033277	abortive mitotic cell cycle	A cell cycle in which mitosis is begun and progresses normally through the end of anaphase, but not completed, resulting in a cell with increased ploidy.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0002244	hematopoietic progenitor cell differentiation	The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0035855	megakaryocyte development	The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow.
	GO:0042267	natural killer cell mediated cytotoxicity	The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
	GO:0050859	negative regulation of B 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 B cell.
	GO:0043407	negative regulation of MAP kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
	GO:0043409	negative regulation of MAPK cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade.
	GO:0042130	negative regulation of T cell proliferation	Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
	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:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0002924	negative regulation of humoral immune response mediated by circulating immunoglobulin	Any process that stops, prevents, or reduces the frequency, rate, or extent of a humoral immune response mediated by circulating immunoglobulin.
	GO:0050732	negative regulation of peptidyl-tyrosine phosphorylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0030168	platelet activation	A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
	GO:0070527	platelet aggregation	The adhesion of one platelet to one or more other platelets via adhesion molecules.
	GO:0030220	platelet formation	The process in which platelets bud from long processes extended by megakaryocytes.
	GO:0033630	positive regulation of cell adhesion mediated by integrin	Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0014068	positive regulation of phosphatidylinositol 3-kinase signaling	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0045577	regulation of B cell differentiation	Any process that modulates the frequency, rate or extent of B cell differentiation.
	GO:0070372	regulation of ERK1 and ERK2 cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:2000045	regulation of G1/S transition of mitotic cell cycle	Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle.
	GO:0051279	regulation of release of sequestered calcium ion into cytosol	Any process that modulates the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
	GO:0060338	regulation of type I interferon-mediated signaling pathway	Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
cellular component
	GO:0042105	alpha-beta T cell receptor complex	A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.

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	1fpr
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	PTN6_HUMAN \| P29350	:	1gwz 1x6c 2b3o 2rmx 2yu7 3ps5 4gry 4grz 4gs0 4hjp 4hjq

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