3JXF - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CA-LIKE DOMAIN OF HUMAN PTPRZ

Authors :   S. Bouyain

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

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Ca-Like Domain, Alternative Splicing, Glycoprotein, Hydrolase, Membrane, Polymorphism, 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 ZETA
	Chains	:	A, B
	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	:	N-TERMINAL CA-LIKE DOMAIN (UNP RESIDUES 34-302)
	Gene	:	HTPZP2, PTPRZ, PTPRZ1, PTPRZ2, PTPZ
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	R-PTP-ZETA, R-PTP-ZETA-2, PROTEIN-TYROSINE PHOSPHATASE RECEPTOR TYPE Z POLYPEPTIDE 1, PROTEIN-TYROSINE PHOSPHATASE RECEPTOR TYPE Z POLYPEPTIDE 2

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3JXF)

Asymmetric Unit

No.	Residues
1	A:56	-	A:240
2	A:133	-	A:264
3	B:56	-	B:240
4	B:133	-	B:264

Asymmetric Unit

No.	Residues
1	Ser A:62	-	Pro A:63
2	Pro A:238	-	Pro A:239
3	Ser B:62	-	Pro B:63
4	Pro B:238	-	Pro B:239

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_2	PS51144	Alpha-carbonic anhydrases profile.	PTPRZ_HUMAN	36-300	2	A:36-300 B:36-300

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.	PTPRZ_HUMAN	36-300	1	A:36-300 -

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.	PTPRZ_HUMAN	36-300	1	- B:36-300

(no "Exon" information available for 3JXF)

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:268
 aligned with PTPRZ_HUMAN | P23471 from UniProtKB/Swiss-Prot  Length:2315

    Alignment length:268
                                    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        
          PTPRZ_HUMAN    34 EEIGWSYTGALNQKNWGKKYPTCNSPKQSPINIDEDLTQVNVNLKKLKFQGWDKTSLENTFIHNTGKTVEINLTNDYRVSGGVSEMVFKASKITFHWGKCNMSSDGSEHSLEGQKFPLEMQIYCFDADRFSSFEEAVKGKGKLRALSILFEVGTEENLDFKAIIDGVESVSRFGKQAALDPFILLNLLPNSTDKYYIYNGSLTSPPCTDTVDWIVFKDTVSISESQLAVFCEVLTMQQSGYVMLMDYLQNNFREQQYKFSRQVFSSYT 301
               SCOP domains d3jxfa_ A: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh......eehhhhhee....eeeeee..........eeee....eeee.....eeeee.....eeeeeeeeee............ee......eeeeeeee......hhhhhhhh...eeeeeeeeee....hhhhhhhhhhhhhh.....eee....hhhhhh......eeeeee..........eeeeee...eeehhhhhhhhhh.eeeeee..eeeeee................ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ALPHA_CA_2  PDB: A:36-300 UniProt: 36-300                                                                                                                                                                                                                                - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxf A  34 EEIGWSYTGALNQKNWGKKYPTCNSPKQSPINIDEDLTQVNVNLKKLKFQGWDKTSLENTFIHNTGKTVEINLTNDYRVSGGVSEMVFKASKITFHWGKCNMSSDGSEHSLEGQKFPLEMQIYCFDADRFSSFEEAVKGKGKLRALSILFEVGTEENLDFKAIIDGVESVSRFGKQAALDPFILLNLLPNSTDKYYIYNGSLTSPPCTDTVDWIVFKDTVSISESQLAVFCEVLTMQQSGYVMLMDYLQNNFREQQYKFSRQVFSSYT 301
                                    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

Chain B from PDB  Type:PROTEIN  Length:271
 aligned with PTPRZ_HUMAN | P23471 from UniProtKB/Swiss-Prot  Length:2315

    Alignment length:271
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
          PTPRZ_HUMAN    31 KLVEEIGWSYTGALNQKNWGKKYPTCNSPKQSPINIDEDLTQVNVNLKKLKFQGWDKTSLENTFIHNTGKTVEINLTNDYRVSGGVSEMVFKASKITFHWGKCNMSSDGSEHSLEGQKFPLEMQIYCFDADRFSSFEEAVKGKGKLRALSILFEVGTEENLDFKAIIDGVESVSRFGKQAALDPFILLNLLPNSTDKYYIYNGSLTSPPCTDTVDWIVFKDTVSISESQLAVFCEVLTMQQSGYVMLMDYLQNNFREQQYKFSRQVFSSYT 301
               SCOP domains d3jxfb_ B: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Carb_anhydrase-3jxfB01 B:38-300                                                                                                                                                                                                                                        - Pfam domains (1)
           Pfam domains (2) -------Carb_anhydrase-3jxfB02 B:38-300                                                                                                                                                                                                                                        - Pfam domains (2)
         Sec.struct. author ..............hhhhhhhhhhhhhh......eehhhhhee....eeeeee..........eeee....eeee.....eeeee.....eeeeeeeeee............ee......eeeeeeee......hhhhhhhh...eeeeeeeeeee...hhhhhhhhhhhhhh.....eee....hhhhhh......eeeeee..........eeeeee...eeeehhhhhhhhh.eeeeee..eeeeee................ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----ALPHA_CA_2  PDB: B:36-300 UniProt: 36-300                                                                                                                                                                                                                                - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxf B  31 PGSEEIGWSYTGALNQKNWGKKYPTCNSPKQSPINIDEDLTQVNVNLKKLKFQGWDKTSLENTFIHNTGKTVEINLTNDYRVSGGVSEMVFKASKITFHWGKCNMSSDGSEHSLEGQKFPLEMQIYCFDADRFSSFEEAVKGKGKLRALSILFEVGTEENLDFKAIIDGVESVSRFGKQAALDPFILLNLLPNSTDKYYIYNGSLTSPPCTDTVDWIVFKDTVSISESQLAVFCEVLTMQQSGYVMLMDYLQNNFREQQYKFSRQVFSSYT 301
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

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)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d3jxfa_	A:
1b	d3jxfb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Carb_anhydrase (168)

Homo sapiens (Human) (157)

1a	Carb_anhydrase-3jxfB01	B:38-300
1b	Carb_anhydrase-3jxfB02	B:38-300

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTPRZ_HUMAN | P23471)

molecular function
	GO:0017134	fibroblast growth factor binding	Interacting selectively and non-covalently with a fibroblast growth factor.
	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: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.
	GO:0005001	transmembrane receptor protein tyrosine phosphatase activity	Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0007413	axonal fasciculation	The collection of axons into a bundle of rods, known as a fascicle.
	GO:0007409	axonogenesis	De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0007417	central nervous system development	The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0002244	hematopoietic progenitor cell differentiation	The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
	GO:0021766	hippocampus development	The progression of the hippocampus over time from its initial formation until its mature state.
	GO:0007611	learning or memory	The acquisition and processing of information and/or the storage and retrieval of this information over time.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0010812	negative regulation of cell-substrate adhesion	Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
	GO:2000171	negative regulation of dendrite development	Any process that stops, prevents, or reduces the frequency, rate or extent of dendrite development.
	GO:0048666	neuron development	The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
	GO:0048709	oligodendrocyte differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:1900149	positive regulation of Schwann cell migration	Any process that activates or increases the frequency, rate or extent of Schwann cell migration.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:1900006	positive regulation of dendrite development	Any process that activates or increases the frequency, rate or extent of dendrite development.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	GO:1901216	positive regulation of neuron death	Any process that activates or increases the frequency, rate or extent of neuron death.
	GO:2001224	positive regulation of neuron migration	Any process that activates or increases the frequency, rate or extent of neuron migration.
	GO:0010976	positive regulation of neuron projection development	Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0048814	regulation of dendrite morphogenesis	Any process that modulates the frequency, rate or extent of dendrite morphogenesis.
	GO:0070445	regulation of oligodendrocyte progenitor proliferation	Any process that modulates the frequency, rate or extent of oligodendrocyte progenitor proliferation.
	GO:0008542	visual learning	Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0043197	dendritic spine	A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0030175	filopodium	Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
	GO:0030426	growth cone	The migrating motile tip of a growing nerve cell axon or dendrite.
	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:0005887	integral component of plasma membrane	The component of the plasma 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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0072534	perineuronal net	A dense extracellular matrix (ECM) structure that forms around many neuronal cell bodies and dendrites late in development and is responsible for synaptic stabilization in the adult brain.
	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.
	GO:0045211	postsynaptic membrane	A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.
	GO:0032587	ruffle membrane	The portion of the plasma membrane surrounding a ruffle.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 3jxf)

	Cis Peptide Bonds
		Pro A:238 - Pro A:239	[ RasMol ]
		Pro B:238 - Pro B:239	[ RasMol ]
		Ser A:62 - Pro A:63	[ RasMol ]
		Ser B:62 - Pro B:63	[ RasMol ]

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Access by PDB/NDB ID
	3jxf
		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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	PTPRZ_HUMAN \| P23471
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	3.1.3.48
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	PTPRZ_HUMAN \| P23471	:	3s97 5awx

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (4, 4)

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