3VQF - JenaLib

Title :   CRYSTAL STRUCTURE ANALYSIS OF THE PDZ DOMAIN DERIVED FROM THE TIGHT JUNCTION REGULATING PROTEIN

Authors :   Y. Akiyoshi, D. Hamada, N. Goda, T. Tenno, H. Narita, A. Nakagawa, M. Fur M. Suzuki, H. Hiroaki

Date :   22 Mar 12 (Deposition) - 27 Mar 13 (Release) - 27 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : A

Keywords :   Pdz Domain, Claudin C-Terminus, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Akiyoshi, Y. Nakakura, D. Hamada, N. Goda, T. Tenno, H. Narita, A. Nakagawa, M. Furuse, M. Suzuki, H. Hiroaki
Structural Basis For Down Regulation Of Tight Junction By Pdz-Domain Containing E3-Ubiquitin Ligase
To Be Published
PubMed: search

Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE LNX
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P3-PRESAT
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SECOND PDZ DOMAIN
	Gene	:	LNX1
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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)
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Chain A from PDB  Type:PROTEIN  Length:85
 aligned with LNX1_MOUSE | O70263 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:85
                                   392       402       412       422       432       442       452       462     
           LNX1_MOUSE   383 SFHVILNKSSPEEQLGIKLVRRVDEPGVFIFNVLNGGVADRHGQLEENDRVLAINGHDLRFGSPESAAHLIQASERRVHLVVSRQ 467
               SCOP domains d3vqfa_ A: automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeee.......eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --PDZ  PDB: A:5-87 UniProt: 385-468                                                   PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3vqf A   3 SFHVILNKSSPEEQLGIKLVRRVDEPGVFIFNVLNGGVADRHGQLEENDRVLAINGHDLRFGSPESAAHLIQASERRVHLVVSRQ  87
                                    12        22        32        42        52        62        72        82

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LNX1_MOUSE | O70263)

molecular function
	GO:0030165	PDZ domain binding	Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
	GO:0006511	ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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Description