2VPH - JenaLib

Asymmetric Unit

Biological Unit 1

Biological Unit 2

Biological Unit 3

collapse

expand

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Description

Title :   CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 4, PDZ DOMAIN

Authors :   A. K. Roos, J. Wang, N. Burgess-Brown, J. M. Elkins, K. Kavanagh, A. C. W. P. Filippakopoulos, C. H. Arrowsmith, J. Weigelt, A. Edwards, F. Von C. Bountra, S. Knapp

Date :   29 Feb 08 (Deposition) - 18 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Protein Phosphatase, Ptpn4, Ptpmeg, Hydrolase, Cytoskeleton, Megakaryocyte, Dephosphorylation, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Roos, J. Wang, N. Burgess-Brown, J. M. Elkins, K. Kavanagh, A. C. W. Pike, P. Filippakopoulos, C. H. Arrowsmith, J. Weigelt, A. Edwards, F. Von Delft, C. Bountra, S. Knapp
Crystal Structure Of The Human Protein Tyrosine Phosphatase, Non-Receptor Type 4, Pdz Domain
To Be Published
PubMed: search

Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4
	Chains	:	A, B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-ROSETTA-PRARE2
	Fragment	:	PDZ DOMAIN, RESIDUES 513-606
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN-TYROSINE PHOSPHATASE MEG1, PTPASE-MEG1, MEG

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

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

Sites (0, 0)

(no "Site" information available for 2VPH)

SS Bonds (0, 0)

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

Cis Peptide Bonds (2, 2)

Asymmetric Unit

No.	Residues
1	Val A:557	-	Pro A:558
2	Val B:557	-	Pro B:558

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PTN4_HUMAN	517-589	2	A:517-589 B:517-589

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PTN4_HUMAN	517-589	2	A:517-589 B:517-589

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PTN4_HUMAN	517-589	1	A:517-589 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PTN4_HUMAN	517-589	1	- B:517-589

Exons (4, 8)

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000263708	1a	ENSE00001202414	chr2:120517207-120517960	754	PTN4_HUMAN	-	0	0	-	-
1.4b	ENST00000263708	4b	ENSE00002161456	chr2:120567413-120567567	155	PTN4_HUMAN	1-46	46	0	-	-
1.5b	ENST00000263708	5b	ENSE00001071386	chr2:120620112-120620219	108	PTN4_HUMAN	47-82	36	0	-	-
1.6	ENST00000263708	6	ENSE00001071393	chr2:120634899-120634941	43	PTN4_HUMAN	83-97	15	0	-	-
1.7b	ENST00000263708	7b	ENSE00001071383	chr2:120635040-120635118	79	PTN4_HUMAN	97-123	27	0	-	-
1.9b	ENST00000263708	9b	ENSE00001071380	chr2:120639362-120639406	45	PTN4_HUMAN	123-138	16	0	-	-
1.10a	ENST00000263708	10a	ENSE00001071395	chr2:120639673-120639725	53	PTN4_HUMAN	138-156	19	0	-	-
1.11b	ENST00000263708	11b	ENSE00001071376	chr2:120640079-120640199	121	PTN4_HUMAN	156-196	41	0	-	-
1.12	ENST00000263708	12	ENSE00001071384	chr2:120643371-120643458	88	PTN4_HUMAN	196-225	30	0	-	-
1.13	ENST00000263708	13	ENSE00001730738	chr2:120658294-120658382	89	PTN4_HUMAN	226-255	30	0	-	-
1.14a	ENST00000263708	14a	ENSE00001694309	chr2:120672755-120672818	64	PTN4_HUMAN	255-276	22	0	-	-
1.15	ENST00000263708	15	ENSE00001803769	chr2:120677645-120677817	173	PTN4_HUMAN	277-334	58	0	-	-
1.16	ENST00000263708	16	ENSE00001640493	chr2:120684174-120684242	69	PTN4_HUMAN	334-357	24	0	-	-
1.17b	ENST00000263708	17b	ENSE00001645678	chr2:120690000-120690125	126	PTN4_HUMAN	357-399	43	0	-	-
1.18a	ENST00000263708	18a	ENSE00001696851	chr2:120692376-120692534	159	PTN4_HUMAN	399-452	54	0	-	-
1.19	ENST00000263708	19	ENSE00001749019	chr2:120702657-120702816	160	PTN4_HUMAN	452-505	54	0	-	-
1.20	ENST00000263708	20	ENSE00001771605	chr2:120703917-120704000	84	PTN4_HUMAN	506-533	28	2	A:513-533 B:0-533 (gaps)	21 22
1.21a	ENST00000263708	21a	ENSE00001594878	chr2:120704094-120704150	57	PTN4_HUMAN	534-552	19	2	A:534-552 B:534-552	19 19
1.22	ENST00000263708	22	ENSE00001621051	chr2:120709549-120709705	157	PTN4_HUMAN	553-605	53	2	A:553-605 B:553-605 (gaps)	53 53
1.23	ENST00000263708	23	ENSE00001731922	chr2:120712733-120712899	167	PTN4_HUMAN	605-660	56	2	A:605-610 B:605-610	6 6
1.24	ENST00000263708	24	ENSE00001660931	chr2:120714420-120714510	91	PTN4_HUMAN	661-691	31	0	-	-
1.25	ENST00000263708	25	ENSE00001797325	chr2:120714592-120714653	62	PTN4_HUMAN	691-711	21	0	-	-
1.26b	ENST00000263708	26b	ENSE00001751186	chr2:120718383-120718529	147	PTN4_HUMAN	712-760	49	0	-	-
1.27	ENST00000263708	27	ENSE00001765275	chr2:120720192-120720320	129	PTN4_HUMAN	761-803	43	0	-	-
1.28	ENST00000263708	28	ENSE00001760145	chr2:120723073-120723221	149	PTN4_HUMAN	804-853	50	0	-	-
1.29b	ENST00000263708	29b	ENSE00001771727	chr2:120725413-120725548	136	PTN4_HUMAN	853-898	46	0	-	-
1.30c	ENST00000263708	30c	ENSE00001703057	chr2:120734560-120741394	6835	PTN4_HUMAN	899-926	28	0	-	-

Sequences/Alignments

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:98
 aligned with PTN4_HUMAN | P29074 from UniProtKB/Swiss-Prot  Length:926

    Alignment length:98
                                   522       532       542       552       562       572       582       592       602        
           PTN4_HUMAN   513 DNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPNAVYDVV 610
               SCOP domains d2vpha_ A: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeeeehhhheeeeeeee...hhhhhh........eeeee..ee....hhhhhhhhhhhhhhh....eeeeee....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:517-589 UniProt: 517-589                                     --------------------- PROSITE
           Transcript 1 (1) Exon 1.20            Exon 1.21a         Exon 1.22  PDB: A:553-605 UniProt: 553-605           ----- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------1.23   Transcript 1 (2)
                 2vph A 513 DNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPNAVESTV 610
                                   522       532       542       552       562       572       582       592       602

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with PTN4_HUMAN | P29074 from UniProtKB/Swiss-Prot  Length:926

    Alignment length:99
                                   521       531       541       551       561       571       581       591       601         
           PTN4_HUMAN   512 HDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPNAVYDVV 610
               SCOP domains d2vphb_ B: a utomated matches                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----PDZ-2vp hB01 B:517-602                                                                -------- Pfam domains (1)
           Pfam domains (2) -----PDZ-2vp hB02 B:517-602                                                                -------- Pfam domains (2)
         Sec.struct. author ....eeeee...-.....eeeeeehhhheeeeeeee...hhhhhh........eeeee..ee....hhhhhhhhhhh.------.eeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: B:517-589 UniProt: 517-589                                     --------------------- PROSITE
           Transcript 1 (1) Exon 1.20 [INCOMPLETE]Exon 1.21a         Exon 1.22  PDB: B:553-605 (gaps) UniProt: 553-605    ----- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------1.23   Transcript 1 (2)
                 2vph B   0 MDNLVLIRMKPD-NGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKAS------ELMLLVRPNAVESTV 610
                            ||     521 | |   531       541       551       561       571       581       | -    |  601         
                            0|       523 |                                                             589    596              
                           513         525

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: PDZ domain (180)

Protein domain: automated matches (53)

Human (Homo sapiens) [TaxId: 9606] (34)

1a	d2vpha_	A:
1b	d2vphb_	B:

CATH Domains (0, 0)

(no "CATH Domain" information available for 2VPH)

Pfam Domains (1, 2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

1a	PDZ-2vphB01	B:517-602
1b	PDZ-2vphB02	B:517-602

Gene Ontology (15, 15)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTN4_HUMAN | P29074)

molecular function
	GO:0008092	cytoskeletal protein binding	Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
	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:0004726	non-membrane spanning protein tyrosine phosphatase activity	Catalysis of the reaction: non-membrane spanning protein tyrosine phosphate + H2O = non-membrane spanning protein tyrosine + phosphate.
	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.
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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: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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2vph)

	Sites
(no "Sites" information available for 2vph)

	Cis Peptide Bonds
		Val A:557 - Pro A:558	[ RasMol ]
		Val B:557 - Pro B:558	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2vph
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PTN4_HUMAN \| P29074
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.3.48
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PTN4_HUMAN \| P29074
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	PTN4_HUMAN \| P29074	:	2cs5 2i75 3nfk 3nfl 5eyz 5ez0

Related Entries Specified in the PDB File

2cs5	SOLUTION STRUCTURE OF PDZ DOMAIN OF PROTEIN TYROSINEPHOSPHATASE, NON-RECEPTOR TYPE 4