1YZ4 - JenaLib

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Title :   CRYSTAL STRUCTURE OF DUSP15

Authors :   S. J. Kim, S. E. Ryu, D. G. Jeong, T. S. Yoon, J. H. Kim, Y. H. Cho, S. K. Jeong, J. W. Lee, J. H. Son

Date :   28 Feb 05 (Deposition) - 01 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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

Reference :   T. S. Yoon, D. G. Jeong, J. H. Kim, Y. H. Cho, J. H. Son, J. W. Lee, S. E. Ryu, S. J. Kim
Crystal Structure Of The Catalytic Domain Of Human Vhy, A Dual-Specificity Protein Phosphatase
Proteins V. 61 694 2005
PubMed-ID: 16170801 | Reference-DOI: 10.1002/PROT.20642
(for further references see the PDB file header)

Molecule 1 - DUAL SPECIFICITY PHOSPHATASE-LIKE 15 ISOFORM A
	Chains	:	A, B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DUSP15

		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 (2, 5)

No.	Name	Count	Type	Full Name
1	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	BOG	1	Ligand/Ion	B-OCTYLGLUCOSIDE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	BOG	-1	Ligand/Ion	B-OCTYLGLUCOSIDE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:38 , GLU A:39 , PHE A:89 , ARG A:94 , HOH A:218 , VAL B:8 , LEU B:9 , VAL B:103 , ALA B:117	BINDING SITE FOR RESIDUE BOG A 210
2	AC2	SOFTWARE	SER A:88 , PHE A:89 , ALA A:90 , GLY A:91 , ILE A:92 , SER A:93 , ARG A:94 , HOH A:215 , HOH A:218	BINDING SITE FOR RESIDUE SO4 A 211
3	AC3	SOFTWARE	SER B:88 , PHE B:89 , ALA B:90 , GLY B:91 , ILE B:92 , SER B:93 , ARG B:94	BINDING SITE FOR RESIDUE SO4 B 158
4	AC4	SOFTWARE	ARG A:52 , ARG A:112 , GLY B:155 , GLU B:156 , SER B:157	BINDING SITE FOR RESIDUE SO4 B 159
5	AC5	SOFTWARE	HIS B:38 , GLU B:39 , SER B:40 , ARG B:94	BINDING SITE FOR RESIDUE SO4 B 160

(no "SS Bond" information available for 1YZ4)

(no "Cis Peptide Bond" information available for 1YZ4)

(no "SAP(SNP)/Variant" information available for 1YZ4)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_DUAL	PS50054	Dual specificity protein phosphatase family profile.	DUS15_HUMAN	5-135	2	A:8-138 B:8-138
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	DUS15_HUMAN	62-120	2	A:65-123 B:65-123
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	DUS15_HUMAN	83-93	2	A:86-96 B:86-96

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.	DUS15_HUMAN	5-135	1	A:8-138 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	DUS15_HUMAN	62-120	1	A:65-123 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	DUS15_HUMAN	83-93	1	A:86-96 -

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.	DUS15_HUMAN	5-135	1	- B:8-138
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	DUS15_HUMAN	62-120	1	- B:65-123
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	DUS15_HUMAN	83-93	1	- B:86-96

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000278979	1c	ENSE00001404816	chr20:30458467-30458379	89	DUS15_HUMAN	1-4	4	2	A:1-4 B:5-7	4 3
1.2e	ENST00000278979	2e	ENSE00001644526	chr20:30457400-30457367	34	DUS15_HUMAN	5-16	12	2	A:8-19 B:8-19	12 12
1.3	ENST00000278979	3	ENSE00001738266	chr20:30454956-30454874	83	DUS15_HUMAN	16-43	28	2	A:19-46 B:19-46	28 28
1.4	ENST00000278979	4	ENSE00001689256	chr20:30452805-30452756	50	DUS15_HUMAN	44-60	17	2	A:47-63 B:47-63	17 17
1.6a	ENST00000278979	6a	ENSE00001618322	chr20:30451784-30451710	75	DUS15_HUMAN	60-85	26	2	A:63-88 B:63-88	26 26
1.7b	ENST00000278979	7b	ENSE00001790094	chr20:30450545-30450374	172	DUS15_HUMAN	85-142	58	2	A:88-145 B:88-145	58 58
1.9	ENST00000278979	9	ENSE00001224518	chr20:30438479-30438415	65	DUS15_HUMAN	143-164	22	0	-	-
1.10	ENST00000278979	10	ENSE00001224513	chr20:30437677-30437541	137	DUS15_HUMAN	164-210	47	2	A:146-153 B:146-153	8 8
1.12	ENST00000278979	12	ENSE00000991589	chr20:30436706-30436609	98	DUS15_HUMAN	210-242	33	2	A:154-156 B:154-157	3 4
1.13	ENST00000278979	13	ENSE00001682152	chr20:30436368-30435440	929	DUS15_HUMAN	243-295	53	0	-	-

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:159
 aligned with DUS15_HUMAN | Q9H1R2 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:231
                               1  4   5                                                                                                                                                                                                                            
                               |  |  -|       14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224 
          DUS15_HUMAN     - ---MTEG---VLPGLYLGNFIDAKDLDQLGRNKITHIISIHESPQPLLQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHCFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGWASSQKGARHRTSKTSGAQCPPMTSATCLLAARVALLSAALVREATGRTAQRCRLSPRAAAERLLGPPPHVAAGWSPDPKYQICLCFGE 225
               SCOP domains d1yz4a_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains -------1yz4A01 A:5-156 Protein tyrosine phosphatase superfamily                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..eeee..hhhhhhhhhhhh...eeeee...........eeeee........hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh--------------------------------------------hhhhhhhh----------------------------hh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------TYR_PHOSPHATASE_DUAL  PDB: A:8-138 UniProt: 5-135                                                                                  ------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:65-123 UniProt: 62-120           --------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
           Transcript 1 (1) ---1.1c---Exon 1.2e   ---------------------------Exon 1.4         ------------------------Exon 1.7b  PDB: A:88-145 UniProt: 85-142                  ---------------------Exon 1.10  PDB: A:146-153 UniProt: 164-210     --------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.3  PDB: A:19-46      ----------------Exon 1.6a  PDB: A:63-88   ---------------------------------------------------------Exon 1.9  PDB: -      ---------------------------------------------Exon 1.12        Transcript 1 (2)
                 1yz4 A  -2 GSHMGNGMTKVLPGLYLGNFIDAKDLDQLGRNKITHIISIHESPQPLLQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHSFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGWASSQK--------------------------------------------LRRQLEER----------------------------FGE 156
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       | -         -         -         -         -  |    153         -         -       155 
                                                                                                                                                                             145                                          146    153                          154

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with DUS15_HUMAN | Q9H1R2 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:229
                               1                                                                                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217         
          DUS15_HUMAN     - ---MTEGVLPGLYLGNFIDAKDLDQLGRNKITHIISIHESPQPLLQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHCFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGWASSQKGARHRTSKTSGAQCPPMTSATCLLAARVALLSAALVREATGRTAQRCRLSPRAAAERLLGPPPHVAAGWSPDPKYQICLCFGEE 226
               SCOP domains d1yz4b _ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ---1yz 4B01 B:5-157 Protein tyrosine phosphatase superfamily                                                                                                                                                                          CATH domains
           Pfam domains (1) -----------DSPc-1yz4B01 B:12-140                                                                                                            ----------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------DSPc-1yz4B02 B:12-140                                                                                                            ----------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....ee-ee..eeeehhhhhhhhhhhhhh...eeee............eeee.........hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhh--------------------------------------------hhhhhhhh----------------------------h... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------TYR_PHOSPHATASE_DUAL  PDB: B:8-138 UniProt: 5-135                                                                                  ------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:65-123 UniProt: 62-120           ---------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) ---1.1cExon 1.2e   ---------------------------Exon 1.4         ------------------------Exon 1.7b  PDB: B:88-145 UniProt: 85-142                  ---------------------Exon 1.10  PDB: B:146-153 UniProt: 164-210     ---------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.3  PDB: B:19-46      ----------------Exon 1.6a  PDB: B:63-88   ---------------------------------------------------------Exon 1.9  PDB: -      ---------------------------------------------Exon 1.12         Transcript 1 (2)
                 1yz4 B   2 GNGMTK-VLPGLYLGNFIDAKDLDQLGRNKITHIISIHESPQPLLQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHSFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGWASSQK--------------------------------------------LRRQLEER----------------------------FGES 157
                                 | |10        20        30        40        50        60        70        80        90       100       110       120       130       140    |    -         -         -         -       146      |  -         -         -     |   
                                 7 8                                                                                                                                      145                                          146    153                          154

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( (-)

)

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	d1yz4a_	A:
1b	d1yz4b_	B:

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	1yz4B01	B:5-157
1b	1yz4A01	A:5-156

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: DSPc (22)

Homo sapiens (Human) (13)

1a	DSPc-1yz4B01	B:12-140
1b	DSPc-1yz4B02	B:12-140

Asymmetric Unit(hide GO term definitions)

Chain A,B (DUS15_HUMAN | Q9H1R2)

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: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: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: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:0046330	positive regulation of JNK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0007179	transforming growth factor beta receptor signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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Ligands, Modified Residues, Ions (2, 5)

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