3RGO - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PTPMT1

Authors :   J. Xiao, J. L. Engel

Date :   08 Apr 11 (Deposition) - 06 Jul 11 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

Chains :   Asym./Biol. Unit : A

Keywords :   Phosphatidylglycerol Phosphate (Pgp) Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Xiao, J. L. Engel, J. Zhang, M. J. Chen, G. Manning, J. E. Dixon
Structural And Functional Analysis Of Ptpmt1, A Phosphatase Required For Cardiolipin Synthesis.
Proc. Natl. Acad. Sci. Usa V. 108 11860 2011
PubMed-ID: 21730175 | Reference-DOI: 10.1073/PNAS.1109290108

Molecule 1 - PROTEIN-TYROSINE PHOSPHATASE MITOCHONDRIAL 1
	Chains	:	A
	EC Number	:	3.1.3.16, 3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PLIP, PTPMT1
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	PTEN-LIKE PHOSPHATASE, PHOSPHOINOSITIDE LIPID PHOSPHATASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:5 , CYS A:102 , LYS A:103 , ALA A:104 , GLY A:105 , ARG A:106 , SER A:107 , ARG A:108 , SER A:109	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	ASN A:42 , THR A:69 , VAL A:70 , ASP A:71 , MET A:72 , THR A:73 , GLY A:74 , ARG A:108	BINDING SITE FOR RESIDUE SO4 A 2

(no "SS Bond" information available for 3RGO)

(no "Cis Peptide Bond" information available for 3RGO)

(no "SAP(SNP)/Variant" information available for 3RGO)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTPM1_MOUSE	109-177	1	A:79-147
2	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPM1_MOUSE	130-140	1	A:100-110

(no "Exon" information available for 3RGO)

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:157
 aligned with PTPM1_MOUSE | Q66GT5 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:157
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       
          PTPM1_MOUSE    37 WYHRIDHTVLLGALPLKNMTRRLVLDENVRGVITMNEEYETRFLCNTSKEWKKAGVEQLRLSTVDMTGVPTLANLHKGVQFALKYQALGQCVYVHCKAGRSRSATMVAAYLIQVHNWSPEEAIEAIAKIRSHISIRPSQLEVLKEFHKEITARAAKN 193
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------DSPc-3rgoA01 A:29-155                                                                                                          -------- Pfam domains
         Sec.struct. author .eee....eeee...hhhhhhhhhhhh.eeeeeee...........hhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:79-147 UniProt: 109-177                    ---------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rgo A   7 WYHRIDHTVLLGALPLKNMTRRLVLDENVRGVITMNEEYETRFLCNTSKEWKKAGVEQLRLSTVDMTGVPTLANLHKGVQFALKYQALGQCVYVHCKAGRSRSATMVAAYLIQVHNWSPEEAIEAIAKIRSHISIRPSQLEVLKEFHKEITARAAKN 163
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

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 3RGO)

(no "CATH Domain" information available for 3RGO)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: DSPc (22)

Mus musculus (Mouse) (2)

DSPc-3rgoA01

A:29-155

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PTPM1_MOUSE | Q66GT5)

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:0008962	phosphatidylglycerophosphatase activity	Catalysis of the reaction: phosphatidylglycerophosphate + H2O = phosphatidylglycerol + phosphate.
	GO:0004439	phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + 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: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:0032049	cardiolipin biosynthetic process	The chemical reactions and pathways resulting in the formation of cardiolipin, 1,3-bis(3-phosphatidyl)glycerol.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0006655	phosphatidylglycerol biosynthetic process	The chemical reactions and pathways resulting in the formation of phosphatidylglycerols, any of a class of phospholipids in which the phosphatidyl group is esterified to the hydroxyl group of glycerol.
	GO:0046488	phosphatidylinositol metabolic process	The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
	GO:0008654	phospholipid biosynthetic process	The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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
	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
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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)

Access by PDB/NDB ID
	3rgo
		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
	PTPM1_MOUSE \| Q66GT5
		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)
	3.1.3.16
		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

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
	PTPM1_MOUSE \| Q66GT5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PTPM1_MOUSE \| Q66GT5	:	3rgq

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (19, 19)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File