3JXG - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CA-LIKE DOMAIN OF MOUSE PTPRG

Authors :   S. Bouyain

Date :   19 Sep 09 (Deposition) - 22 Dec 09 (Release) - 16 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Ca-Like Domain, Glycoprotein, Hydrolase, Membrane, Phosphoprotein, Protein Phosphatase, Transmembrane, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bouyain, D. J. Watkins
The Protein Tyrosine Phosphatases Ptprz And Ptprg Bind To Distinct Members Of The Contactin Family Of Neural Recognition Molecules.
Proc. Natl. Acad. Sci. Usa V. 107 2443 2010
PubMed-ID: 20133774 | Reference-DOI: 10.1073/PNAS.0911235107

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE GAMMA
	Chains	:	A, B, C, D
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32
	Expression System Strain	:	ORIGAMI2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CARBONIC ANHYDRASE-LIKE DOMAIN (UNP RESIDUES 55- 320)
	Gene	:	PTPRG
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	PROTEIN-TYROSINE PHOSPHATASE GAMMA, R-PTP-GAMMA

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3JXG)

(no "Site" information available for 3JXG)

Asymmetric Unit

No.	Residues
1	A:78	-	A:261
2	B:78	-	B:261
3	C:78	-	C:261
4	D:78	-	D:261

Asymmetric Unit

No.	Residues
1	Ser A:84	-	Pro A:85
2	Pro A:259	-	Pro A:260
3	Ser B:84	-	Pro B:85
4	Pro B:259	-	Pro B:260
5	Ser C:84	-	Pro C:85
6	Pro C:259	-	Pro C:260
7	Ser D:84	-	Pro D:85
8	Pro D:259	-	Pro D:260

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	PTPRG_MOUSE	58-321	4	A:58-320 B:58-320 C:58-320 D:58-320

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	PTPRG_MOUSE	58-321	1	A:58-320 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	PTPRG_MOUSE	58-321	1	- B:58-320 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	PTPRG_MOUSE	58-321	1	- - C:58-320 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	PTPRG_MOUSE	58-321	1	- - - D:58-320

(no "Exon" information available for 3JXG)

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:257
 aligned with PTPRG_MOUSE | Q05909 from UniProtKB/Swiss-Prot  Length:1442

    Alignment length:263
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317   
          PTPRG_MOUSE    58 PYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARVGDEYQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNPDDFDSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTEQQDHVKSVEYLRNNFRPQQALNDRVVSKS 320
               SCOP domains d3jxga_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh......eehhhhhee.......eee..........eeee....eeee.....eee.......eeeeeeeeee...........ee......eeeeeeee......hhhhhhhh...eeeeeeeeee....hhhhhhhhhhhhh......eee....hhhhhh......eeeeee..........eeeeee...eeehhhhhhhhhh.ee..------..ee................ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ALPHA_CA_2  PDB: A:58-320 UniProt: 58-321                                                                                                                                                                                                                               PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxg A  58 PYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARVGDEYQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNPDDFDSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTE------SVEYLRNNFRPQQALNDRVVSKS 320
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   |     -|      307       317   
                                                                                                                                                                                                                                                                   291    298

Chain B from PDB  Type:PROTEIN  Length:259
 aligned with PTPRG_MOUSE | Q05909 from UniProtKB/Swiss-Prot  Length:1442

    Alignment length:263
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317   
          PTPRG_MOUSE    58 PYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARVGDEYQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNPDDFDSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTEQQDHVKSVEYLRNNFRPQQALNDRVVSKS 320
               SCOP domains d3jxgb_ B: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh......eehhhhhee.......eee..........eeee....eeee.....eee.......eeeeeeeeee...........ee......eeeeeeee......hhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhhh......eee....hhhhhh......eeeeee..........eeeeee...eeeehhhhhhhh..eeee.----.eeee................ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ALPHA_CA_2  PDB: B:58-320 UniProt: 58-321                                                                                                                                                                                                                               PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxg B  58 PYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARVGDEYQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNPDDFDSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTEQ----KSVEYLRNNFRPQQALNDRVVSKS 320
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287    |  297       307       317   
                                                                                                                                                                                                                                                                    292  297

Chain C from PDB  Type:PROTEIN  Length:264
 aligned with PTPRG_MOUSE | Q05909 from UniProtKB/Swiss-Prot  Length:1442

    Alignment length:264
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316    
          PTPRG_MOUSE    57 DPYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARVGDEYQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNPDDFDSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTEQQDHVKSVEYLRNNFRPQQALNDRVVSKS 320
               SCOP domains d3jxgc_ C: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh......eehhhhh.........eee..........eeee....eeee.....eee.......eeeeeeeeee...........ee......eeeeeeee......hhhhhhhh...eeeeeeeeeee...hhhhhhhhhhhhh......eee....hhhhhh......eeeeee..........eeeeee...eeeehhhhhhhhh.eeeeee..eeeeee................ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -ALPHA_CA_2  PDB: C:58-320 UniProt: 58-321                                                                                                                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jxg C  57 DPYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARVGDEYQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNPDDFDSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTEQQDHVKSVEYLRNNFRPQQALNDRVVSKS 320
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316

Chain D from PDB  Type:PROTEIN  Length:259
 aligned with PTPRG_MOUSE | Q05909 from UniProtKB/Swiss-Prot  Length:1442

    Alignment length:263
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317   
          PTPRG_MOUSE    58 PYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARVGDEYQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNPDDFDSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTEQQDHVKSVEYLRNNFRPQQALNDRVVSKS 320
               SCOP domains d3jxgd_ D: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Carb_anhydrase-3jxgD01 D:60-320                                                                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) --Carb_anhydrase-3jxgD02 D:60-320                                                                                                                                                                                                                                       Pfam domains (2)
           Pfam domains (3) --Carb_anhydrase-3jxgD03 D:60-320                                                                                                                                                                                                                                       Pfam domains (3)
           Pfam domains (4) --Carb_anhydrase-3jxgD04 D:60-320                                                                                                                                                                                                                                       Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh......eehhhhhee.......eee..........eeee....eeee.....eee.......eeeeeeeeee...........ee......eeeeeeee..---.hhhhhhhh...eeeeeeeeeee...hhhhhhhhhhhhhh.....eee....hhhhhh......eeeeee..........eeeeee...eeeehhhhhhhhh.eeeee.-..eeeee................ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ALPHA_CA_2  PDB: D:58-320 UniProt: 58-321                                                                                                                                                                                                                               PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxg D  58 PYWAYSGAYGPEHWVTSSVSCGGSHQSPIDILDHHARVGDEYQELQLDGFDNESSNKTWMKNTGKTVAILLKDDYFVSGAGLPGRFKAEKVEFHWGHSNGSAGSEHSVNGRRFPVEMQIFFYNP---DSFQTAISENRIIGAMAIFFQVSPRDNSALDPIIHGLKGVVHHEKETFLDPFILRDLLPASLGSYYRYTGSLTTPPCSEIVEWIVFRRPVPISYHQLEAFYSIFTTEQQ-HVKSVEYLRNNFRPQQALNDRVVSKS 320
                                    67        77        87        97       107       117       127       137       147       157       167       177   |   187       197       207       217       227       237       247       257       267       277       287     | 297       307       317   
                                                                                                                                                     181 185                                                                                                         293 |                         
                                                                                                                                                                                                                                                                       295

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Carbonic anhydrase (525)

Superfamily: Carbonic anhydrase (525)

Family: automated matches (12)

Protein domain: automated matches (12)

Mouse (Mus musculus) [TaxId: 10090] (2)

1a	d3jxga_	A:
1b	d3jxgb_	B:
1c	d3jxgc_	C:
1d	d3jxgd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Carb_anhydrase] (168)

Family: Carb_anhydrase (168)

Mus musculus (Mouse) (6)

1a	Carb_anhydrase-3jxgD01	D:60-320
1b	Carb_anhydrase-3jxgD02	D:60-320
1c	Carb_anhydrase-3jxgD03	D:60-320
1d	Carb_anhydrase-3jxgD04	D:60-320

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PTPRG_MOUSE | Q05909)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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:0010633	negative regulation of epithelial cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
	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:1901998	toxin transport	The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3jxg)

	Sites
(no "Sites" information available for 3jxg)

	Cis Peptide Bonds
		Pro A:259 - Pro A:260	[ RasMol ]
		Pro B:259 - Pro B:260	[ RasMol ]
		Pro C:259 - Pro C:260	[ RasMol ]
		Pro D:259 - Pro D:260	[ RasMol ]
		Ser A:84 - Pro A:85	[ RasMol ]
		Ser B:84 - Pro B:85	[ RasMol ]
		Ser C:84 - Pro C:85	[ RasMol ]
		Ser D:84 - Pro D:85	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

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Access by PDB/NDB ID
	3jxg
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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Access by UniProt ID/Accession number
	PTPRG_MOUSE \| Q05909
		Comparative Protein Structure Models	:	ModBase
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	3.1.3.48
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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	PTPRG_MOUSE \| Q05909
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UniProtKB/Swiss-Prot
	PTPRG_MOUSE \| Q05909	:	3kld 5e5u

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (13, 13)

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Related Entries Specified in the PDB File