3N8I - JenaLib

Title :   CRYSTAL STRUCTURE OF THE A ISOFORM OF HUMAN CYTOPLASMIC PROTEIN TYROSINE PHOSPHATASE (HCPTP-A) IN COMPLEX WITH 1-NAPHTYLACETIC ACID

Authors :   K. T. Homan, D. Balasubramaniam, C. V. Stauffacher

Date :   28 May 10 (Deposition) - 07 Dec 11 (Release) - 07 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Tyrosine Phosphatase, Hydrolase, Protein-Ligand Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. T. Homan, D. Balasubramaniam, C. V. Stauffacher
Structural Characterization Of A Secondary Binding Site On Low Molecular Weight Protein Tyrosine Phosphatases
To Be Published
PubMed: search

Compounds

Molecule 1 - LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE
	Chains	:	A
	EC Number	:	3.1.3.48, 3.1.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11D
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ACP1, APC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LMW-PTPASE, LMW-PTP, LOW MOLECULAR WEIGHT CYTOSOLIC ACID PHOSPHATASE, RED CELL ACID PHOSPHATASE 1, ADIPOCYTE ACID PHOSPHATASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (0, 0)

Exons (6, 6)

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2c	ENST00000272065	2c	ENSE00001907935	chr2:264872-265007	136	PPAC_HUMAN	1-15	15	1	A:4-14	11
1.5	ENST00000272065	5	ENSE00001617949	chr2:271866-271939	74	PPAC_HUMAN	15-39	25	1	A:14-38	25
1.6b	ENST00000272065	6b	ENSE00001704285	chr2:272037-272150	114	PPAC_HUMAN	40-77	38	1	A:39-76	38
1.8c	ENST00000272065	8c	ENSE00001653664	chr2:275140-275201	62	PPAC_HUMAN	78-98	21	1	A:77-97	21
1.9	ENST00000272065	9	ENSE00001680540	chr2:276980-277085	106	PPAC_HUMAN	98-133	36	1	A:97-132	36
1.10f	ENST00000272065	10f	ENSE00001380378	chr2:277227-278283	1057	PPAC_HUMAN	134-158	25	1	A:133-157	25

Sequences/Alignments

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:154
 aligned with PPAC_HUMAN | P24666 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:154
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154    
           PPAC_HUMAN     5 ATKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNPPDYRGQSCMKRHGIPMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH 158
               SCOP domains d3n8ia_ A: Tyrosine phosphatase                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhh.hhh.eeeeeee..........hhhhhhhhhhh...........hhhhhhhh.eeee.hhhhhhhhhhhhh.......eeee.hhhh.............hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --N--------------------------------------------------------------------------------------------------R------------------------------F--------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2c  ------------------------Exon 1.6b  PDB: A:39-76 UniProt: 40-77Exon 1.8c            -----------------------------------Exon 1.10f  PDB: A:133-15 Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.5  PDB: A:14-38   ----------------------------------------------------------Exon 1.9  PDB: A:97-132             ------------------------- Transcript 1 (2)
                 3n8i A   4 ATKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNPPDYRGQSCMKRHGIPMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH 157
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153

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, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PPAC_HUMAN | P24666)

molecular function
	GO:0003993	acid phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
	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: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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Visualization

Interactive Views

Asymmetric/Biological 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
		NLA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3n8i)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3n8i
		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
	PPAC_HUMAN \| P24666
		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)
	3.1.3.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	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
	PPAC_HUMAN \| P24666
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description