2PPI - JenaLib

Title :   STRUCTURE OF THE BTB (TRAMTRACK AND BRIC A BRAC) DOMAIN OF HUMAN GIGAXONIN

Authors :   A. Amos, A. P. Turnbull, J. Tickle, T. Keates, A. Bullock, P. Savitsky, N Brown, J. E. Debreczeni, E. Ugochukwu, C. Umeano, A. C. W. Pike, E. Papagrigoriou, M. Sundstrom, C. H. Arrowsmith, J. Weigelt, A. Edwa Delft, S. Knapp, Structural Genomics Consortium (Sgc)

Date :   30 Apr 07 (Deposition) - 08 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Btb Domain, Protein Degradation, Structural Genomics, Structural Genomics Consortium, Sgc, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Amos, A. P. Turnbull, J. Tickle, T. Keates, A. Bullock, P. Savitsky, N. Burgess-Brown, J. E. Debreczeni, E. Ugochukwu, C. Umeano, A. C. W. Pike, E. Papagrigoriou, M. Sundstrom, C. H. Arrowsmith, J. Weigelt, A. Edwards, F. Von Delft, S. Knapp
Structure Of The Btb (Tramtrack And Bric A Brac) Domain Of Human Gigaxonin.
To Be Published
PubMed: search

Compounds

Molecule 1 - GIGAXONIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3) WITH PRARE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	BTB DOMAIN
	Gene	:	GAN, GAN1, KLHL16
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	KELCH-LIKE PROTEIN 16

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 (8, 8)

Asymmetric Unit (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010759	R	15	S	GAN_HUMAN	Disease (GAN1)	119485093	A	R	15	S
2	UniProt	VAR_054113	A	51	P	GAN_HUMAN	Disease (GAN1)	750258209	A	A	51	P
3	UniProt	VAR_010760	S	52	G	GAN_HUMAN	Disease (GAN1)	---	A	S	52	G
4	UniProt	VAR_010761	S	79	L	GAN_HUMAN	Disease (GAN1)	---	A	S	79	L
5	UniProt	VAR_010762	V	82	F	GAN_HUMAN	Disease (GAN1)	---	A	V	82	F
6	UniProt	VAR_015680	I	86	F	GAN_HUMAN	Disease (GAN1)	---	A	I	86	F
7	UniProt	VAR_054114	Y	89	C	GAN_HUMAN	Disease (GAN1)	---	A	Y	89	C
8	UniProt	VAR_073289	I	102	T	GAN_HUMAN	Disease	---	A	I	102	T

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

Biological Unit 1 (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010759	R	15	S	GAN_HUMAN	Disease (GAN1)	119485093	A	R	15	S
2	UniProt	VAR_054113	A	51	P	GAN_HUMAN	Disease (GAN1)	750258209	A	A	51	P
3	UniProt	VAR_010760	S	52	G	GAN_HUMAN	Disease (GAN1)	---	A	S	52	G
4	UniProt	VAR_010761	S	79	L	GAN_HUMAN	Disease (GAN1)	---	A	S	79	L
5	UniProt	VAR_010762	V	82	F	GAN_HUMAN	Disease (GAN1)	---	A	V	82	F
6	UniProt	VAR_015680	I	86	F	GAN_HUMAN	Disease (GAN1)	---	A	I	86	F
7	UniProt	VAR_054114	Y	89	C	GAN_HUMAN	Disease (GAN1)	---	A	Y	89	C
8	UniProt	VAR_073289	I	102	T	GAN_HUMAN	Disease	---	A	I	102	T

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

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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:118
 aligned with GAN_HUMAN | Q9H2C0 from UniProtKB/Swiss-Prot  Length:597

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            GAN_HUMAN     1 MAEGSAVSDPQHAARLLRALSSFREESRFCDAHLVLDGEEIPVQKNILAAASPYIRTKLNYNPPKDDGSTYKIELEGISVMVMREILDYIFSGQIRLNEDTIQDVVQAADLLLLTDLKTLCCEFL 125
               SCOP domains d2ppia_ A: automated matc  hes                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------BTB-2p  piA01 A:20-125                                                                                     Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh..--....eeeee..eeeeehhhhhhhhhhhhhhhhhhh.-----...eee....hhhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------S-----------------------------------PG--------------------------L--F---F--C------------T----------------------- SAPs(SNPs)
                    PROSITE -----------------------------BTB  PDB: A:30-99 UniProt: 30-99                                      -------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ppi A   1 YFQSMAVSDPQHAARLLRALSSFRE--RFCDAHLVLDGEEIPVQKNILAAASPYIRTKLNYNP-----STYKIELEGISVMVMREILDYIFSGQIRLNEDTIQDVVQAADLLLLTDLKTLCCEFL 125
                                    10        20    |  |30        40        50        60  |     70        80        90       100       110       120     
                                                   25 28                                 63    69

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (GAN_HUMAN | Q9H2C0)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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.
biological process
	GO:0007010	cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	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.
cellular component
	GO:0031463	Cul3-RING ubiquitin ligase complex	A ubiquitin ligase complex in which a cullin from the Cul3 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a BTB-domain-containing protein.
	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.

Visualization

Interactive Views

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
(no "Ligands, Modified Residues, Ions" information available for 2ppi)

	Sites
(no "Sites" information available for 2ppi)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ppi)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2ppi
		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
	GAN_HUMAN \| Q9H2C0
		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)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	256850
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

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
	GAN_HUMAN \| Q9H2C0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description