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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF PTPMT1 IN COMPLEX WITH PI(5)P

Authors :   J. Xiao, J. L. Engel

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

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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
	Mutation	:	YES
	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, 1)

No.	Name	Count	Type	Full Name
1	5P5	1	Ligand/Ion	(2R)-3-{[(S)-HYDROXY{[(1R,2R,3R,4R,5S,6R)-2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1,2-DIYLDIBUTANOATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:21 , HOH A:83 , TRP A:105 , LEU A:118 , MET A:170 , SER A:200 , LYS A:201 , ALA A:202 , GLY A:203 , ARG A:204 , SER A:205 , ARG A:206 , ARG A:240	BINDING SITE FOR RESIDUE 5P5 A 300

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

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

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

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:177-245
2	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTPM1_MOUSE	130-140	1	A:198-208

(no "Exon" information available for 3RGQ)

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:156
 aligned with PTPM1_MOUSE | Q66GT5 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:156
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185      
          PTPM1_MOUSE    36 DWYHRIDHTVLLGALPLKNMTRRLVLDENVRGVITMNEEYETRFLCNTSKEWKKAGVEQLRLSTVDMTGVPTLANLHKGVQFALKYQALGQCVYVHCKAGRSRSATMVAAYLIQVHNWSPEEAIEAIAKIRSHISIRPSQLEVLKEFHKEITARAA 191
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------DSPc-3rgqA01 A:127-253                                                                                                         ------ Pfam domains
         Sec.struct. author ..eee....eeee...hhhhhhhhhhh..eeeeee..hhhhhh....hhhhhhhh..eeee..........hhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:177-245 UniProt: 109-177                   -------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rgq A 104 DWYHRIDHTVLLGALPLKNMTRRLVLDENVRGVITMNEEYETRFLCNTSKEWKKAGVEQLRLSTVDMTGVPTLANLHKGVQFALKYQALGQCVYVHSKAGRSRSATMVAAYLIQVHNWSPEEAIEAIAKIRSHISIRPSQLEVLKEFHKEITARAA 259
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

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 3RGQ)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: DSPc (22)

Mus musculus (Mouse) (2)

DSPc-3rgqA01

A:127-253

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.

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	3rgq
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	PTPM1_MOUSE \| Q66GT5
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	3.1.3.16
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	3.1.3.48
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	PTPM1_MOUSE \| Q66GT5	:	3rgo

Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

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