2G6Z - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF HUMAN DUSP5

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

Date :   26 Feb 06 (Deposition) - 16 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B,C

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

Reference :   D. G. Jeong, Y. H. Cho, T. S. Yoon, J. H. Kim, S. E. Ryu, S. J. Kim
Crystal Structure Of The Catalytic Domain Of Human Dusp5, A Dual Specificity Map Kinase Protein Phosphatase
Proteins V. 66 253 2007
PubMed-ID: 17078075 | Reference-DOI: 10.1002/PROT.21224
(for further references see the PDB file header)

Molecule 1 - DUAL SPECIFICITY PROTEIN PHOSPHATASE 5
	Chains	:	A, B, C
	EC Number	:	3.1.3.48, 3.1.3.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 174-384
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DUSP5, DUAL SPECIFICITY PROTEIN PHOSPHATASE HVH3, TYROSINE-PROTEIN PHOSPHATASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:263 , GLU A:264 , ALA A:265 , GLY A:266 , ILE A:267 , SER A:268 , ARG A:269	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	HOH A:8 , ARG A:213 , ARG A:214 , GLU A:264 , ARG A:269	BINDING SITE FOR RESIDUE SO4 A 502
3	AC3	SOFTWARE	HOH B:29 , SER B:263 , GLU B:264 , ALA B:265 , GLY B:266 , ILE B:267 , SER B:268 , ARG B:269	BINDING SITE FOR RESIDUE SO4 B 503
4	AC4	SOFTWARE	HOH B:31 , ARG B:213 , ARG B:214 , GLU B:264 , ARG B:269	BINDING SITE FOR RESIDUE SO4 B 504
5	AC5	SOFTWARE	SER C:263 , GLU C:264 , ALA C:265 , GLY C:266 , ILE C:267 , SER C:268 , ARG C:269	BINDING SITE FOR RESIDUE SO4 C 505
6	AC6	SOFTWARE	SER C:212 , ARG C:213 , ARG C:214 , GLU C:264 , ARG C:269	BINDING SITE FOR RESIDUE SO4 C 506

Asymmetric/Biological Unit

No.	Residues
1	A:197	-	A:219
2	B:197	-	B:219
3	C:197	-	C:219

(no "Cis Peptide Bond" information available for 2G6Z)

Asymmetric/Biological Unit (2, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_059777	A	220	T	DUS5_HUMAN	Polymorphism	1889566	A/B/C	M	220	T
2	UniProt	VAR_059778	A	220	V	DUS5_HUMAN	Polymorphism	1889565	A/B/C	M	220	V

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

Asymmetric/Biological 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.	DUS5_HUMAN	178-318	3	A:178-318 B:178-318 C:178-318
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	DUS5_HUMAN	240-297	3	A:240-297 B:240-297 C:240-297
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	DUS5_HUMAN	261-271	3	A:261-271 B:261-271 C:261-271

Asymmetric/Biological Unit (3, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000369583	1a	ENSE00001450398	chr10:112257596-112258258	663	DUS5_HUMAN	1-127	127	0	-	-
1.2a	ENST00000369583	2a	ENSE00000723795	chr10:112262479-112262627	149	DUS5_HUMAN	127-176	50	2	A:174-176 (gaps) - C:174-176 (gaps)	15 - 15
1.4b	ENST00000369583	4b	ENSE00000723796	chr10:112266693-112266912	220	DUS5_HUMAN	177-250	74	3	A:177-250 B:178-250 C:177-250	74 73 74
1.5b	ENST00000369583	5b	ENSE00001450392	chr10:112269778-112271302	1525	DUS5_HUMAN	250-384	135	3	A:250-320 B:250-320 C:250-319	71 71 70

Asymmetric/Biological 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:147
 aligned with DUS5_HUMAN | Q16690 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:159
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
           DUS5_HUMAN   162 GKPVVNVSYRPAYDQGGPVEILPFLYLGSAYHASKCEFLANLHITALLNVSRRTSEACATHLHYKWIPVEDSHTADISSHFQEAIDFIDCVREKGGKVLVHCEAGISRSPTICMAYLMKTKQFRLKEAFDYIKQRRSMVSPNFGFMGQLLQYESEILPS 320
               SCOP domains d2            g6za_ A: automated matches                                                                                                                        SCOP domains
               CATH domains 2g            6zA00 A:174-320 Protein tyrosine phosphatase superfamily                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------....eeee..eeeeehhhhhhhhhhhhhh..eeee.............eeee..........hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------T---------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------V---------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) ----------------TYR_PHOSPHATASE_DUAL  PDB: A:178-318 UniProt: 178-318                                                                                        -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:240-297 UniProt: 240-297        ----------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.2a      Exon 1.4b  PDB: A:177-250 UniProt: 177-250                                ---------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.5b  PDB: A:250-320 UniProt: 250-384 [INCOMPLETE]                 Transcript 1 (2)
                 2g6z A 174 GS------------HMGPVEILPFLYLGSAYHASKCEFLANLHITALLNVSRRTSEACMTHLHYKWIPVEDSHTADISSHFQEAIDFIDCVREKGGKVLVHSEAGISRSPTICMAYLMKTKQFRLKEAFDYIKQRRSMVSPNFGFMGQLLQYESEILPS 320
                             |       -    |  181       191       201       211       221       231       241       251       261       271       281       291       301       311         
                             |          176                                                                                                                                                
                           175

Chain B from PDB  Type:PROTEIN  Length:143
 aligned with DUS5_HUMAN | Q16690 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:143
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317   
           DUS5_HUMAN   178 GPVEILPFLYLGSAYHASKCEFLANLHITALLNVSRRTSEACATHLHYKWIPVEDSHTADISSHFQEAIDFIDCVREKGGKVLVHCEAGISRSPTICMAYLMKTKQFRLKEAFDYIKQRRSMVSPNFGFMGQLLQYESEILPS 320
               SCOP domains d2g6zb_ B: automated matches                                                                                                                    SCOP domains
               CATH domains 2g6zB00 B:178-320 Protein tyrosine phosphatase superfamily                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeehhhhhhhhhhhhhh..eeee.............eeee..........hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------T---------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------V---------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) TYR_PHOSPHATASE_DUAL  PDB: B:178-318 UniProt: 178-318                                                                                        -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:240-297 UniProt: 240-297        ----------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.4b  PDB: B:178-250 UniProt: 177-250 [INCOMPLETE]                  ---------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------Exon 1.5b  PDB: B:250-320 UniProt: 250-384 [INCOMPLETE]                 Transcript 1 (2)
                 2g6z B 178 GPVEILPFLYLGSAYHASKCEFLANLHITALLNVSRRTSEACMTHLHYKWIPVEDSHTADISSHFQEAIDFIDCVREKGGKVLVHSEAGISRSPTICMAYLMKTKQFRLKEAFDYIKQRRSMVSPNFGFMGQLLQYESEILPS 320
                                   187       197       207       217       227       237       247       257       267       277       287       297       307       317

Chain C from PDB  Type:PROTEIN  Length:146
 aligned with DUS5_HUMAN | Q16690 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:158
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        
           DUS5_HUMAN   162 GKPVVNVSYRPAYDQGGPVEILPFLYLGSAYHASKCEFLANLHITALLNVSRRTSEACATHLHYKWIPVEDSHTADISSHFQEAIDFIDCVREKGGKVLVHCEAGISRSPTICMAYLMKTKQFRLKEAFDYIKQRRSMVSPNFGFMGQLLQYESEILP 319
               SCOP domains d2            g6zc_ C: automated matches                                                                                                                       SCOP domains
               CATH domains 2g            6zC00 C:174-319 Protein tyrosine phosphatase superfamily                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------....eeee..eeeee.hhhhhhhhhhhhh..eeee.............eeee..........hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------T--------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------V--------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) ----------------TYR_PHOSPHATASE_DUAL  PDB: C:178-318 UniProt: 178-318                                                                                        - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: C:240-297 UniProt: 240-297        ---------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------ PROSITE (3)
           Transcript 1 (1) Exon 1.2a      Exon 1.4b  PDB: C:177-250 UniProt: 177-250                                --------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.5b  PDB: C:250-319 UniProt: 250-384 [INCOMPLETE]                Transcript 1 (2)
                 2g6z C 174 GS------------HMGPVEILPFLYLGSAYHASKCEFLANLHITALLNVSRRTSEACMTHLHYKWIPVEDSHTADISSHFQEAIDFIDCVREKGGKVLVHSEAGISRSPTICMAYLMKTKQFRLKEAFDYIKQRRSMVSPNFGFMGQLLQYESEILP 319
                             |       -    |  181       191       201       211       221       231       241       251       261       271       281       291       301       311        
                           175          176

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/Biological Unit

Classes(

)

Folds(

)

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	d2g6za_	A:
1b	d2g6zb_	B:
1c	d2g6zc_	C:

Asymmetric/Biological 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	2g6zA00	A:174-320
1b	2g6zC00	C:174-319
1c	2g6zB00	B:178-320

(no "Pfam Domain" information available for 2G6Z)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (DUS5_HUMAN | Q16690)

molecular function
	GO:0017017	MAP kinase tyrosine/serine/threonine phosphatase activity	Catalysis of the reaction: MAP kinase serine/threonine/tyrosine phosphate + H2O = MAP kinase serine/threonine/tyrosine + phosphate.
	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:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0001706	endoderm formation	The formation of the endoderm during gastrulation.
	GO:0000188	inactivation of MAPK activity	Any process that terminates the activity of the active enzyme MAP kinase.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

Asymmetric/Biological Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (3, 3)

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