2NT2 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SLINGSHOT PHOSPHATASE 2

Authors :   S. K. Jung, D. G. Jeong, T. S. Yoon, J. H. Kim, S. E. Ryu, S. J. Kim

Date :   06 Nov 06 (Deposition) - 05 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Alpha/Beta Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. K. Jung, D. G. Jeong, T. S. Yoon, J. H. Kim, S. E. Ryu, S. J. Kim
Crystal Structure Of Human Slingshot Phosphatase 2.
Proteins V. 68 408 2007
PubMed-ID: 17427953 | Reference-DOI: 10.1002/PROT.21399
(for further references see the PDB file header)

Molecule 1 - PROTEIN PHOSPHATASE SLINGSHOT HOMOLOG 2
	Chains	:	A, B, C
	EC Number	:	3.1.3.48, 3.1.3.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 305-449
	Gene	:	SSH2, KIAA1725, SSH2L
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SLINGSHOT PHOSPHATASE 2, SSH-2L, HSSH-2L

		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)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:361 , SER A:392 , LYS A:393 , MET A:394 , GLY A:395 , VAL A:396 , SER A:397 , ARG A:398	BINDING SITE FOR RESIDUE SO4 A 101
2	AC2	SOFTWARE	ASP B:361 , SER B:392 , LYS B:393 , MET B:394 , GLY B:395 , VAL B:396 , SER B:397 , ARG B:398	BINDING SITE FOR RESIDUE SO4 B 101
3	AC3	SOFTWARE	HOH C:66 , ASP C:361 , SER C:392 , LYS C:393 , MET C:394 , GLY C:395 , VAL C:396 , SER C:397 , ARG C:398	BINDING SITE FOR RESIDUE SO4 C 101

(no "SS Bond" information available for 2NT2)

(no "Cis Peptide Bond" information available for 2NT2)

(no "SAP(SNP)/Variant" information available for 2NT2)

Asymmetric Unit (3, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_DUAL	PS50054	Dual specificity protein phosphatase family profile.	SSH2_HUMAN	307-447	3	A:307-447 B:307-447 C:307-447
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	SSH2_HUMAN	372-426	3	A:372-426 B:372-426 C:372-426
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	SSH2_HUMAN	390-400	3	A:390-400 B:390-400 C:390-400

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_DUAL	PS50054	Dual specificity protein phosphatase family profile.	SSH2_HUMAN	307-447	1	A:307-447 - -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	SSH2_HUMAN	372-426	1	A:372-426 - -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	SSH2_HUMAN	390-400	1	A:390-400 - -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_DUAL	PS50054	Dual specificity protein phosphatase family profile.	SSH2_HUMAN	307-447	1	- B:307-447 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	SSH2_HUMAN	372-426	1	- B:372-426 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	SSH2_HUMAN	390-400	1	- B:390-400 -

Biological Unit 3 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_DUAL	PS50054	Dual specificity protein phosphatase family profile.	SSH2_HUMAN	307-447	1	- - C:307-447
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	SSH2_HUMAN	372-426	1	- - C:372-426
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	SSH2_HUMAN	390-400	1	- - C:390-400

Asymmetric Unit (4, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000269033	1a	ENSE00001878927	chr17:28257170-28256956	215	SSH2_HUMAN	1-21	21	0	-	-
1.2	ENST00000269033	2	ENSE00001227577	chr17:28120955-28120912	44	SSH2_HUMAN	22-36	15	0	-	-
1.3	ENST00000269033	3	ENSE00001227617	chr17:28030080-28029977	104	SSH2_HUMAN	36-71	36	0	-	-
1.4	ENST00000269033	4	ENSE00001227612	chr17:28022541-28022477	65	SSH2_HUMAN	71-92	22	0	-	-
1.5	ENST00000269033	5	ENSE00001302334	chr17:28011702-28011581	122	SSH2_HUMAN	93-133	41	0	-	-
1.6	ENST00000269033	6	ENSE00001227597	chr17:28004759-28004691	69	SSH2_HUMAN	133-156	24	0	-	-
1.7	ENST00000269033	7	ENSE00001227587	chr17:28003903-28003838	66	SSH2_HUMAN	156-178	23	0	-	-
1.9	ENST00000269033	9	ENSE00001227567	chr17:27999147-27998953	195	SSH2_HUMAN	178-243	66	0	-	-
1.10	ENST00000269033	10	ENSE00001227557	chr17:27994241-27994148	94	SSH2_HUMAN	243-274	32	0	-	-
1.11	ENST00000269033	11	ENSE00001227550	chr17:27994013-27993885	129	SSH2_HUMAN	275-317	43	3	A:307-317 B:307-317 C:307-317	11 11 11
1.12	ENST00000269033	12	ENSE00001128700	chr17:27982625-27982579	47	SSH2_HUMAN	318-333	16	3	A:318-333 B:318-333 C:318-333	16 16 16
1.13	ENST00000269033	13	ENSE00001128689	chr17:27977818-27977672	147	SSH2_HUMAN	333-382	50	3	A:333-382 B:333-382 C:333-382	50 50 50
1.14a	ENST00000269033	14a	ENSE00001295166	chr17:27975362-27975162	201	SSH2_HUMAN	382-449	68	3	A:382-448 B:382-448 C:382-448	67 67 67
1.15	ENST00000269033	15	ENSE00000947602	chr17:27963820-27962986	835	SSH2_HUMAN	449-727	279	0	-	-
1.16	ENST00000269033	16	ENSE00001290380	chr17:27959949-27952956	6994	SSH2_HUMAN	728-1423	696	0	-	-

Asymmetric Unit

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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
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Chain A from PDB  Type:PROTEIN  Length:142
 aligned with SSH2_HUMAN | Q76I76 from UniProtKB/Swiss-Prot  Length:1423

    Alignment length:142
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446  
           SSH2_HUMAN   307 SPTQIFEHVFLGSEWNASNLEDLQNRGVRYILNVTREIDNFFPGVFEYHNIRVYDEEATDLLAYWNDTYKFISKAKKHGSKCLVHCKMGVSRSASTVIAYAMKEYGWNLDRAYDYVKERRTVTKPNPSFMRQLEEYQGILLA 448
               SCOP domains d2nt2a_ A: automated matches                                                                                                                   SCOP domains
               CATH domains 2nt2A00 A:307-448 Protein tyrosine phosphatase superfamily                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeehhhhhhhhhhhhhh.eeeeee.............eeee..........hhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TYR_PHOSPHATASE_DUAL  PDB: A:307-447 UniProt: 307-447                                                                                        - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:372-426 UniProt: 372-426     ---------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
           Transcript 1 (1) Exon 1.11  Exon 1.12       ------------------------------------------------Exon 1.14a  PDB: A:382-448 UniProt: 382-449 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.13  PDB: A:333-382 UniProt: 333-382        ------------------------------------------------------------------ Transcript 1 (2)
                 2nt2 A 307 SPTQIFEHVFLGSEWNASNLEDLQNRGVRYILNVTREIDNFFPGVFEYHNIRVYDEEATDLLAYWNDTYKFISKAKKHGSKCLVHSKMGVSRSASTVIAYAMKEYGWNLDRAYDYVKERRTVTKPNPSFMRQLEEYQGILLA 448
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with SSH2_HUMAN | Q76I76 from UniProtKB/Swiss-Prot  Length:1423

    Alignment length:142
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446  
           SSH2_HUMAN   307 SPTQIFEHVFLGSEWNASNLEDLQNRGVRYILNVTREIDNFFPGVFEYHNIRVYDEEATDLLAYWNDTYKFISKAKKHGSKCLVHCKMGVSRSASTVIAYAMKEYGWNLDRAYDYVKERRTVTKPNPSFMRQLEEYQGILLA 448
               SCOP domains d2nt2b_ B: automated matches                                                                                                                   SCOP domains
               CATH domains 2nt2B00 B:307-448 Protein tyrosine phosphatase superfamily                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeehhhhhhhhhhhhhhheeeeee.............eeee..........hhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TYR_PHOSPHATASE_DUAL  PDB: B:307-447 UniProt: 307-447                                                                                        - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:372-426 UniProt: 372-426     ---------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
           Transcript 1 (1) Exon 1.11  Exon 1.12       ------------------------------------------------Exon 1.14a  PDB: B:382-448 UniProt: 382-449 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.13  PDB: B:333-382 UniProt: 333-382        ------------------------------------------------------------------ Transcript 1 (2)
                 2nt2 B 307 SPTQIFEHVFLGSEWNASNLEDLQNRGVRYILNVTREIDNFFPGVFEYHNIRVYDEEATDLLAYWNDTYKFISKAKKHGSKCLVHSKMGVSRSASTVIAYAMKEYGWNLDRAYDYVKERRTVTKPNPSFMRQLEEYQGILLA 448
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with SSH2_HUMAN | Q76I76 from UniProtKB/Swiss-Prot  Length:1423

    Alignment length:142
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446  
           SSH2_HUMAN   307 SPTQIFEHVFLGSEWNASNLEDLQNRGVRYILNVTREIDNFFPGVFEYHNIRVYDEEATDLLAYWNDTYKFISKAKKHGSKCLVHCKMGVSRSASTVIAYAMKEYGWNLDRAYDYVKERRTVTKPNPSFMRQLEEYQGILLA 448
               SCOP domains d2nt2c_ C: automated matches                                                                                                                   SCOP domains
               CATH domains 2nt2C00 C:307-448 Protein tyrosine phosphatase superfamily                                                                                     CATH domains
           Pfam domains (1) --------DSPc-2nt2C01 C:315-445                                                                                                             --- Pfam domains (1)
           Pfam domains (2) --------DSPc-2nt2C02 C:315-445                                                                                                             --- Pfam domains (2)
           Pfam domains (3) --------DSPc-2nt2C03 C:315-445                                                                                                             --- Pfam domains (3)
         Sec.struct. author ..eeee..eeeehhhhhhhhhhhhhhheeeeee.............eeee..........hhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TYR_PHOSPHATASE_DUAL  PDB: C:307-447 UniProt: 307-447                                                                                        - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: C:372-426 UniProt: 372-426     ---------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
           Transcript 1 (1) Exon 1.11  Exon 1.12       ------------------------------------------------Exon 1.14a  PDB: C:382-448 UniProt: 382-449 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.13  PDB: C:333-382 UniProt: 333-382        ------------------------------------------------------------------ Transcript 1 (2)
                 2nt2 C 307 SPTQIFEHVFLGSEWNASNLEDLQNRGVRYILNVTREIDNFFPGVFEYHNIRVYDEEATDLLAYWNDTYKFISKAKKHGSKCLVHSKMGVSRSASTVIAYAMKEYGWNLDRAYDYVKERRTVTKPNPSFMRQLEEYQGILLA 448
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446

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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(

)

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	d2nt2a_	A:
1b	d2nt2b_	B:
1c	d2nt2c_	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)

Human (Homo sapiens) (196)

1a	2nt2A00	A:307-448
1b	2nt2B00	B:307-448
1c	2nt2C00	C:307-448

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: DSPc (22)

Homo sapiens (Human) (13)

1a	DSPc-2nt2C01	C:315-445
1b	DSPc-2nt2C02	C:315-445
1c	DSPc-2nt2C03	C:315-445

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (SSH2_HUMAN | Q76I76)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	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.
	GO:0008138	protein tyrosine/serine/threonine phosphatase activity	Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	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.
	GO:0008064	regulation of actin polymerization or depolymerization	Any process that modulates the frequency, rate or extent of the assembly or disassembly of actin filaments by the addition or removal of actin monomers from a filament.
	GO:0050770	regulation of axonogenesis	Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron.
	GO:0010591	regulation of lamellipodium assembly	Any process that modulates the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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