2YF0 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   HUMAN MYOTUBULARIN RELATED PROTEIN 6 (MTMR6)

Authors :   M. Moche, L. Tresaugues, C. H. Arrowsmith, H. Berglund, C. Bountra, R. C A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Jo T. Karlberg, T. Kotenyova, E. Kouznetsova, T. Nyman, C. Persson, H. Sc P. Schutz, M. I. Siponen, A. G. Thorsell, S. Vandenberg, E. Wahlberg, J M. Welin, P. Nordlund

Date :   31 Mar 11 (Deposition) - 13 Apr 11 (Release) - 13 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

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

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

Reference :   M. Moche, L. Tresaugues, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Johansson, T. Karlberg, T. Kotenyova, E. Kouznetsova, T. Nyman, C. Persson, H. Schuler, P. Schutz, M. I. Siponen, A. G. Thorsell, S. Vandenberg, E. Wahlberg, J. Weigelt, M. Welin, P. Nordlund
Crystal Structure Of Human Mtmr6
To Be Published
PubMed: search

Molecule 1 - MYOTUBULARIN-RELATED PROTEIN 6
	Chains	:	A
	EC Number	:	3.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3 PRARE
	Expression System Vector	:	PNIC-CH2
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	MAMMALIAN GENE COLLECTION

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

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

Biological Unit 1 (1, 2)

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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:335 , CYS A:336 , SER A:337 , ASP A:338 , GLY A:339 , TRP A:340 , ASP A:341 , ARG A:342 , THR A:343	BINDING SITE FOR RESIDUE SO4 A1506

(no "SS Bond" information available for 2YF0)

Asymmetric Unit

No.	Residues
1	Val A:139	-	Pro A:140
2	Arg A:240	-	Pro A:241

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057143	A	131	T	MTMR6_HUMAN	Polymorphism	34885345	A	A	131	T
2	UniProt	VAR_024583	I	319	V	MTMR6_HUMAN	Polymorphism	7995033	A	V	319	V

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

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_057143	A	131	T	MTMR6_HUMAN	Polymorphism	34885345	A	A	131	T
2	UniProt	VAR_024583	I	319	V	MTMR6_HUMAN	Polymorphism	7995033	A	V	319	V

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PPASE_MYOTUBULARIN	PS51339	Myotubularin phosphatase domain.	MTMR6_HUMAN	124-499	1	A:124-499
2	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	MTMR6_HUMAN	334-344	1	A:334-344

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PPASE_MYOTUBULARIN	PS51339	Myotubularin phosphatase domain.	MTMR6_HUMAN	124-499	2	A:124-499
2	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	MTMR6_HUMAN	334-344	2	A:334-344

(no "Exon" information available for 2YF0)

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:487
 aligned with MTMR6_HUMAN | Q9Y217 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:502
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503  
          MTMR6_HUMAN     4 IRTTKVEQVKLLDRFSTSNKSLTGTLYLTATHLLFIDSHQKETWILHHHIASVEKLALTTSGCPLVIQCKNFRTVHFIVPRERDCHDIYNSLLQLSKQAKYEDLYAFSYNPKQNDSERLQGWQLIDLAEEYKRMGVPNSHWQLSDANRDYKICETYPRELYVPRIASKPIIVGSSKFRSKGRFPVLSYYHQDKEAAICRCSQPLSGFSARCLEDEHLLQAISKANPVNRYMYVMDTRPKLNAMANRAAGKGYENEDNYSNIRFQFVGIENIHVMRSSLQKLLEVNGTKGLSVNDFYSGLESSGWLRHIKAVMDAAIFLAKAITVENASVLVHCSDGWDRTSQVCSLGSLLLDSYYRTIKGFMVLIEKDWISFGHKFSERCGQLDGDPKEVSPVFTQFLECVWHLTEQFPQAFEFSEAFLLQIHEHIHSCQFGNFLGNCQKEREELKLKEKTYSLWPFLLEDQKKYLNPLYSSESHRFTVLEPNTVSFNFKFWRNMYHQFDRT 505
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------        ---------------------------------------------------------------------------------------------------------------------------------Myotub-related-2yf0A02 A:153-269                                                                                     ------------------------------------------------------------Y_phosphatase_m-2yf0A01 A:330-384                      --------------------------------------------------------------------------------------------   -------------------------- Pfam domains
         Sec.struct. author .eeeeeee....--------..eeeeee...eeeeee....eeeee...eeeeee.......eeeeeee....eeeeee.hhhhhhhhhhhhhhhh.......hhhhh......hhhhhhhhh..hhhhhhhhh......eeeehhhh...........eeee...hhhhhhhhhhhhhhhh..eeeee......eeee...........hhhhhhhhhhhhhhh.....eeeee.......----..............eeeee....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh....hhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..........hhhhhhhhhhhhhh..hhhhhh.hhhhhh.......---...............hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------PPASE_MYOTUBULARIN  PDB: A:124-499 UniProt: 124-499                                                                                                                                                                                                                                                                                                                                     ------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yf0 A   4 IRTTKVEQVKLL--------SLTGTLYLTATHLLFIDSHQKETWILHHHIASVEKLALTTSGCPLVIQCKNFRTVHFIVPRERDCHDIYNSLLQLSKQAKYEDLYAFSYNPKQNDSERLQGWQLIDLAEEYKRMGVPNSHWQLSDANRDYKICETYPRELYVPRIASKPIIVGSSKFRSKGRFPVLSYYHQDKEAAICRCSQPLSGFSARCLEDEHLLQAISKANPVNRYMYVMDTRPKLNA----AAGKGYENEDNYSNIRFQFVGIENIHVMRSSLQKLLEVNGTKGLSVNDFYSGLESSGWLRHIKAVMDAAVFLAKAITVENASVLVHCSDGWDRTSQVCSLGSLLLDSYYRTIKGFMVLIEKDWISFGHKFSERCGQLDGDPKEVSPVFTQFLECVWHLTEQFPQAFEFSEAFLLQIHEHIHSCQFGNFLGNCQKEREELKLKEKTYSLWPFLLEDQKKYLNPLYSSE---FTVLEPNTVSFNFKFWRNMYHQFDRT 505
                                    13 |       -|       33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 |    |253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473  |   |483       493       503  
                                      15       24                                                                                                                                                                                                                          245  250                                                                                                                                                                                                                               476 480

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 2YF0)

(no "CATH Domain" information available for 2YF0)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: Y_phosphatase_m (5)

Homo sapiens (Human) (5)

Y_phosphatase_m-2yf0A01

A:330-384

Clan: no clan defined [family: Myotub-related] (5)

Family: Myotub-related (5)

Homo sapiens (Human) (5)

Myotub-related-2yf0A02

A:153-269

Asymmetric Unit(hide GO term definitions)

Chain A (MTMR6_HUMAN | Q9Y217)

molecular function
	GO:0015269	calcium-activated potassium channel activity	Enables the calcium concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient.
	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:0052866	phosphatidylinositol phosphate phosphatase activity	Catalysis of the reaction: phosphatidylinositol phosphate(n) + H2O = phosphatidylinositol phosphate(n-1) + phosphate. This reaction is the removal of a phosphate group from a phosphatidylinositol phosphate.
	GO:0052629	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H2O = a 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate + 2 H+.
	GO:0004438	phosphatidylinositol-3-phosphatase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3-phosphate + H2O = 1-phosphatidyl-1D-myo-inositol + phosphate.
	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:0004722	protein serine/threonine phosphatase activity	Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
	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:0006661	phosphatidylinositol biosynthetic process	The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
	GO:0046856	phosphatidylinositol dephosphorylation	The process of removing one or more phosphate groups from a phosphatidylinositol.
	GO:0071805	potassium ion transmembrane transport	A process in which a potassium ion is transported from one side of a membrane to the other.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	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 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 ]

	Cis Peptide Bonds
		Arg A:240 - Pro A:241	[ RasMol ]
		Val A:139 - Pro A:140	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	2yf0
		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
	MTMR6_HUMAN \| Q9Y217
		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.-
		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
	MTMR6_HUMAN \| Q9Y217
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2YF0)

(no "Related Entries Specified in the PDB File" available for 2YF0)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 2)

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