3LNY - JenaLib

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Title :   SECOND PDZ DOMAIN FROM HUMAN PTP1E IN COMPLEX WITH RA-GEF2 PEPTIDE

Authors :   J. Zhang, A. Chang, H. Ke, G. N. Phillips Jr. , A. L. Lee, Center For Euk Structural Genomics (Cesg)

Date :   03 Feb 10 (Deposition) - 23 Mar 10 (Release) - 28 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (6x)

Keywords :   Pdz2, Structural Genomics, Protein Structure Initiative, Psi-2, Center For Eukaryotic Structural Genomics, Cesg, Cytoskeleton, Cell Membrane, Guanine-Nucleotide Releasing Factor, Signaling Protein- Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Zhang, P. J. Sapienza, H. Ke, A. Chang, S. R. Hengel, H. Wang, G. N. Phillips, A. L. Lee
Crystallographic And Nuclear Magnetic Resonance Evaluation Of The Impact Of Peptide Binding To The Second Pdz Domain O Protein Tyrosine Phosphatase 1E.
Biochemistry V. 49 9280 2010
PubMed-ID: 20839809 | Reference-DOI: 10.1021/BI101131F

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 13
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ2 DOMAIN
	Gene	:	PTPN13, PNP1, PTP1E, PTPL1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN-TYROSINE PHOSPHATASE 1E, PTP-E1, HPTPE1, PTP-BAS, PROTEIN-TYROSINE PHOSPHATASE PTPL1, FAS-ASSOCIATED PROTEIN-TYROSINE PHOSPHATASE 1, FAP-1

Molecule 2 - RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 6
	Chains	:	B
	Engineered	:	YES
	Fragment	:	C-TERMINAL RESIDUES 1596-1601
	Gene	:	RAPGEF6, PDZGEF2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PDZ DOMAIN-CONTAINING GUANINE NUCLEOTIDE EXCHANGE FACTOR 2, PDZ-GEF2, RA-GEF-2

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (6x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

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

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	SCN	6	Ligand/Ion	THIOCYANATE ION
2	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:62 , GLY A:63 , HIS A:86 , HOH A:251 , HOH A:307	BINDING SITE FOR RESIDUE SCN A 97
2	AC2	SOFTWARE	GLU A:76 , THR A:77 , ASN A:80 , HOH A:121 , HOH A:132 , HOH A:162	BINDING SITE FOR RESIDUE SO4 A 98
3	AC3	SOFTWARE	ALA A:12 , GLN A:83 , VAL A:84	BINDING SITE FOR RESIDUE SO4 A 99

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

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

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016200	L	1419	P	PTN13_HUMAN	Polymorphism	749353184	A	L	59	P

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

Biological Unit 1 (1, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016200	L	1419	P	PTN13_HUMAN	Polymorphism	749353184	A	L	59	P

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PTN13_HUMAN	1093-1179 1368-1453 1501-1589 1788-1869 1883-1966	1	- A:8-93 - - -

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	PTN13_HUMAN	1093-1179 1368-1453 1501-1589 1788-1869 1883-1966	6	- A:8-93 - - -

(no "Exon" information available for 3LNY)

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
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Chain A from PDB  Type:PROTEIN  Length:94
 aligned with PTN13_HUMAN | Q12923 from UniProtKB/Swiss-Prot  Length:2485

    Alignment length:94
                                  1370      1380      1390      1400      1410      1420      1430      1440      1450    
         PTN13_HUMAN   1361 PKPGDIFEVELAKNDNSLGISVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVETLRNTGQVVHLLLEKGQS 1454
               SCOP domains d3lnya_ A: Phosphatase hPTP1e                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------PDZ-3lnyA01 A:8-90                                                                 ---- Pfam domains
         Sec.struct. author .....eeeeeee.......eeeee.....hhhh.eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------P----------------------------------- SAPs(SNPs)
                    PROSITE -------PDZ  PDB: A:8-93 UniProt: 1368-1453                                                   - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                3lny A    1 PKPGDIFEVELAKNDNSLGISVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVETLRNTGQVVHLLLEKGQS   94
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:6
 aligned with RPGF6_HUMAN | Q8TEU7 from UniProtKB/Swiss-Prot  Length:1601

    Alignment length:6
         RPGF6_HUMAN   1596 EQVSAV 1601
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eeee Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                3lny B    3 EQVSAV    8

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: PDZ domain (180)

Protein domain: Phosphatase hPTP1e (10)

Human (Homo sapiens) [TaxId: 9606] (7)

d3lnya_

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

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

PDZ-3lnyA01

A:8-90

Asymmetric Unit(hide GO term definitions)

Chain A (PTN13_HUMAN | Q12923)

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:0036312	phosphatidylinositol 3-kinase regulatory subunit binding	Interacting selectively and non-covalently with a regulatory subunit of phosphatidylinositol 3-kinase. The regulatory subunit associates with the catalytic subunit to regulate both its activity and subcellular location.
	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.
	GO:0014066	regulation of phosphatidylinositol 3-kinase signaling	Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
cellular component
	GO:0044297	cell body	The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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.
	GO:0030027	lamellipodium	A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	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.
	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.

Chain B (RPGF6_HUMAN | Q8TEU7)

molecular function
	GO:0030742	GTP-dependent 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) using energy from the hydrolysis of GTP.
	GO:0017016	Ras GTPase binding	Interacting selectively and non-covalently with any member of the Ras superfamily of monomeric GTPases.
	GO:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0070300	phosphatidic acid binding	Interacting selectively and non-covalently with phosphatidic acid, any of a class of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
	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).
biological process
	GO:0007265	Ras protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
	GO:0090557	establishment of endothelial intestinal barrier	The establishment of a barrier between endothelial cell layers of the intestine to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
	GO:0030033	microvillus assembly	Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0072659	protein localization to plasma membrane	A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
	GO:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	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:0030139	endocytic vesicle	A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
	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.

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	3lny
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	PTN13_HUMAN \| Q12923
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	PTN13_HUMAN \| Q12923
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UniProtKB/Swiss-Prot
	PTN13_HUMAN \| Q12923	:	1d5g 1q7x 1wch 2m0z 2m10 3lnx 3pdz 5glj
	RPGF6_HUMAN \| Q8TEU7	:	2d93

(no "Related Entries Specified in the PDB File" available for 3LNY)

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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