2GWO - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TMDP

Authors :   S. J. Kim, S. E. Ryu, J. H. Kim

Date :   05 May 06 (Deposition) - 20 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

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

Reference :   S. J. Kim, D. G. Jeong, T. S. Yoon, J. H. Son, S. K. Cho, S. E. Ryu, J. H. Kim
Crystal Structure Of Human Tmdp, A Testis-Specific Dual Specificity Protein Phosphatase: Implications For Substrate Specificity
Proteins V. 66 239 2007
PubMed-ID: 17044055 | Reference-DOI: 10.1002/PROT.21197
(for further references see the PDB file header)

Molecule 1 - DUAL SPECIFICITY PROTEIN PHOSPHATASE 13
	Chains	:	A, B, C, D
	EC Number	:	3.1.3.48, 3.1.3.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DUSP13, TMDP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TESTIS- AND SKELETAL-MUSCLE-SPECIFIC DSP, DUAL SPECIFICITY PHOSPHATASE SKRP4, TMDP

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2GWO)

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

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

Asymmetric Unit (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057130	R	62	Q	DS13B_HUMAN	Polymorphism	16932004	A/B/C/D	R	62	Q
2	UniProt	VAR_025431	C	156	Y	DS13B_HUMAN	Polymorphism	3088142	A/B/C/D	C	156	Y
3	UniProt	VAR_057131	R	190	G	DS13B_HUMAN	Polymorphism	16931996	A/B/C/D	R	190	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057130	R	62	Q	DS13B_HUMAN	Polymorphism	16932004	A	R	62	Q
2	UniProt	VAR_025431	C	156	Y	DS13B_HUMAN	Polymorphism	3088142	A	C	156	Y
3	UniProt	VAR_057131	R	190	G	DS13B_HUMAN	Polymorphism	16931996	A	R	190	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057130	R	62	Q	DS13B_HUMAN	Polymorphism	16932004	B	R	62	Q
2	UniProt	VAR_025431	C	156	Y	DS13B_HUMAN	Polymorphism	3088142	B	C	156	Y
3	UniProt	VAR_057131	R	190	G	DS13B_HUMAN	Polymorphism	16931996	B	R	190	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057130	R	62	Q	DS13B_HUMAN	Polymorphism	16932004	C	R	62	Q
2	UniProt	VAR_025431	C	156	Y	DS13B_HUMAN	Polymorphism	3088142	C	C	156	Y
3	UniProt	VAR_057131	R	190	G	DS13B_HUMAN	Polymorphism	16931996	C	R	190	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057130	R	62	Q	DS13B_HUMAN	Polymorphism	16932004	D	R	62	Q
2	UniProt	VAR_025431	C	156	Y	DS13B_HUMAN	Polymorphism	3088142	D	C	156	Y
3	UniProt	VAR_057131	R	190	G	DS13B_HUMAN	Polymorphism	16931996	D	R	190	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_DUAL	PS50054	Dual specificity protein phosphatase family profile.	DS13B_HUMAN	45-192	4	A:45-192 B:45-192 C:45-192 D:45-192
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	DS13B_HUMAN	114-172	4	A:114-172 B:114-172 C:114-172 D:114-172
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	DS13B_HUMAN	136-146	4	A:136-146 B:136-146 C:136-146 D:136-146

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.	DS13B_HUMAN	45-192	1	A:45-192 - - -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	DS13B_HUMAN	114-172	1	A:114-172 - - -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	DS13B_HUMAN	136-146	1	A:136-146 - - -

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.	DS13B_HUMAN	45-192	1	- B:45-192 - -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	DS13B_HUMAN	114-172	1	- B:114-172 - -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	DS13B_HUMAN	136-146	1	- B:136-146 - -

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.	DS13B_HUMAN	45-192	1	- - C:45-192 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	DS13B_HUMAN	114-172	1	- - C:114-172 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	DS13B_HUMAN	136-146	1	- - C:136-146 -

Biological Unit 4 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_DUAL	PS50054	Dual specificity protein phosphatase family profile.	DS13B_HUMAN	45-192	1	- - - D:45-192
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	DS13B_HUMAN	114-172	1	- - - D:114-172
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	DS13B_HUMAN	136-146	1	- - - D:136-146

(no "Exon" information available for 2GWO)

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:169
 aligned with DS13B_HUMAN | Q9UII6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:169
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184         
          DS13B_HUMAN    25 PPTLASLQRLLWVRQAATLNHIDEVWPSLFLGDAYAARDKSKLIQLGITHVVNAAAGKFQVDTGAKFYRGMSLEYYGIEADDNPFFDLSVYFLPVARYIRAALSVPQGRVLVHCAMGVSRSATLVLAFLMICENMTLVEAIQTVQAHRNICPNSGFLRQLQVLDNRLGR 193
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2gwoA00 A:25-193 Protein tyrosine phosphatase superfamily                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eee.eeeee..eeeehhhhhhhhhhhhhh...eeee.........hhhhhh.....eeee..........hhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------Q---------------------------------------------------------------------------------------------Y---------------------------------G--- SAPs(SNPs)
                PROSITE (1) --------------------TYR_PHOSPHATASE_DUAL  PDB: A:45-192 UniProt: 45-192                                                                                                 - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:114-172 UniProt: 114-172         --------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gwo A  25 PPTLASLQRLLWVRQAATLNHIDEVWPSLFLGDAYAARDKSKLIQLGITHVVNAAAGKFQVDTGAKFYRGMSLEYYGIEADDNPFFDLSVYFLPVARYIRAALSVPQGRVLVHCAMGVSRSATLVLAFLMICENMTLVEAIQTVQAHRNICPNSGFLRQLQVLDNRLGR 193
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with DS13B_HUMAN | Q9UII6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:169
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184         
          DS13B_HUMAN    25 PPTLASLQRLLWVRQAATLNHIDEVWPSLFLGDAYAARDKSKLIQLGITHVVNAAAGKFQVDTGAKFYRGMSLEYYGIEADDNPFFDLSVYFLPVARYIRAALSVPQGRVLVHCAMGVSRSATLVLAFLMICENMTLVEAIQTVQAHRNICPNSGFLRQLQVLDNRLGR 193
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2gwoB00 B:25-193 Protein tyrosine phosphatase superfamily                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....eee.eeeee..eeeehhhhhhhhhhhhhhh..eeee.........hhhhhh.....eeee.........hhhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------Q---------------------------------------------------------------------------------------------Y---------------------------------G--- SAPs(SNPs)
                PROSITE (1) --------------------TYR_PHOSPHATASE_DUAL  PDB: B:45-192 UniProt: 45-192                                                                                                 - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:114-172 UniProt: 114-172         --------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gwo B  25 PPTLASLQRLLWVRQAATLNHIDEVWPSLFLGDAYAARDKSKLIQLGITHVVNAAAGKFQVDTGAKFYRGMSLEYYGIEADDNPFFDLSVYFLPVARYIRAALSVPQGRVLVHCAMGVSRSATLVLAFLMICENMTLVEAIQTVQAHRNICPNSGFLRQLQVLDNRLGR 193
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184

Chain C from PDB  Type:PROTEIN  Length:174
 aligned with DS13B_HUMAN | Q9UII6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:174
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    
          DS13B_HUMAN    25 PPTLASLQRLLWVRQAATLNHIDEVWPSLFLGDAYAARDKSKLIQLGITHVVNAAAGKFQVDTGAKFYRGMSLEYYGIEADDNPFFDLSVYFLPVARYIRAALSVPQGRVLVHCAMGVSRSATLVLAFLMICENMTLVEAIQTVQAHRNICPNSGFLRQLQVLDNRLGRETGRF 198
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2gwoC00 C:25-198 Protein tyrosine phosphatase superfamily                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eee.eeeee..eeeehhhhhhhhhhhhhhh..eeee.........hhhhhh.....eeee..........hhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------Q---------------------------------------------------------------------------------------------Y---------------------------------G-------- SAPs(SNPs)
                PROSITE (1) --------------------TYR_PHOSPHATASE_DUAL  PDB: C:45-192 UniProt: 45-192                                                                                                 ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: C:114-172 UniProt: 114-172         -------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------TYR_PHOSPHA---------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gwo C  25 PPTLASLQRLLWVRQAATLNHIDEVWPSLFLGDAYAARDKSKLIQLGITHVVNAAAGKFQVDTGAKFYRGMSLEYYGIEADDNPFFDLSVYFLPVARYIRAALSVPQGRVLVHCAMGVSRSATLVLAFLMICENMTLVEAIQTVQAHRNICPNSGFLRQLQVLDNRLGRETGRF 198
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

Chain D from PDB  Type:PROTEIN  Length:174
 aligned with DS13B_HUMAN | Q9UII6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:174
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194    
          DS13B_HUMAN    25 PPTLASLQRLLWVRQAATLNHIDEVWPSLFLGDAYAARDKSKLIQLGITHVVNAAAGKFQVDTGAKFYRGMSLEYYGIEADDNPFFDLSVYFLPVARYIRAALSVPQGRVLVHCAMGVSRSATLVLAFLMICENMTLVEAIQTVQAHRNICPNSGFLRQLQVLDNRLGRETGRF 198
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2gwoD00 D:25-198 Protein tyrosine phosphatase superfamily                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eee.eeeee..eeeehhhhhhhhhhhhhhh..eeee.........hhhhhh.....eeee..........hhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------Q---------------------------------------------------------------------------------------------Y---------------------------------G-------- SAPs(SNPs)
                PROSITE (1) --------------------TYR_PHOSPHATASE_DUAL  PDB: D:45-192 UniProt: 45-192                                                                                                 ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: D:114-172 UniProt: 114-172         -------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------TYR_PHOSPHA---------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gwo D  25 PPTLASLQRLLWVRQAATLNHIDEVWPSLFLGDAYAARDKSKLIQLGITHVVNAAAGKFQVDTGAKFYRGMSLEYYGIEADDNPFFDLSVYFLPVARYIRAALSVPQGRVLVHCAMGVSRSATLVLAFLMICENMTLVEAIQTVQAHRNICPNSGFLRQLQVLDNRLGRETGRF 198
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

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 2GWO)

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	2gwoC00	C:25-198
1b	2gwoD00	D:25-198
1c	2gwoA00	A:25-193
1d	2gwoB00	B:25-193

(no "Pfam Domain" information available for 2GWO)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DS13B_HUMAN | Q9UII6)

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:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.

Asymmetric Unit
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(no "Sites" information available for 2gwo)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gwo)

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(no "Related Entries Specified in the PDB File" available for 2GWO)

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