1LTX

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ltxa1	All alpha proteins	alpha-alpha superhelix	Protein prenylyltransferase	Protein prenylyltransferase	Rab geranylgeranyltransferase alpha-subunit, N-terminal domain	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1ltxa2	All beta proteins	C2 domain-like	Rab geranylgeranyltransferase alpha-subunit, insert domain	Rab geranylgeranyltransferase alpha-subunit, insert domain	Rab geranylgeranyltransferase alpha-subunit, insert domain	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1ltxa3	Alpha and beta proteins (a/b)	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	L domain-like	Rab geranylgeranyltransferase alpha-subunit, C-terminal domain	Rab geranylgeranyltransferase alpha-subunit, C-terminal domain	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C [auth R]	d1ltxr1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	GDI-like N domain	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C [auth R]	d1ltxr2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	GDI-like	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1ltxb_	All alpha proteins	alpha/alpha toroid	Terpenoid cyclases/Protein prenyltransferases	Protein prenyltransferases	Rab geranylgeranyltransferase, beta subunit	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	L domain-like	8043989	3001010	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein prenylyltransferase	8038637	3001312	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rab geranylgeranyltransferase alpha-subunit, insert domain	8040730	3001017	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Protein prenylyltransferase	8038637	3001312	SCOP2B (2022-06-29)
C [auth R]	SCOP2B Superfamily	Flavoreductase-like	8044604	3000055	SCOP2B (2022-06-29)
C [auth R]	SCOP2B Superfamily	GDI isoprenoid-binding domain-like	8091669	3002533	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Terpenoid cyclases/Protein prenyltransferases	8040875	3001024	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RabGGT_insert	e1ltxA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: RabGGT_insert	ECOD (1.6)
A	LRR_9	e1ltxA3	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_9	ECOD (1.6)
A	PPTA	e1ltxA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PPTA	ECOD (1.6)
C [auth R]	KOG4405	e1ltxR1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: KOG4405	ECOD (1.6)
C [auth R]	GDI_1st	e1ltxR2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: GDI_1st	ECOD (1.6)
B	SQHop_cyclase_C	e1ltxB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: SQHop_cyclase_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.120	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Protein prenylyltransferase	CATH (4.3.0)
A	2.60.40.1130	Mainly Beta	Sandwich	Immunoglobulin-like	Rab geranylgeranyltransferase alpha-subunit, insert domain	CATH (4.3.0)
A	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
C [auth R]	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
C [auth R]	3.30.519.10	Alpha Beta	2-Layer Sandwich	Guanine Nucleotide Dissociation Inhibitor	domain 2	CATH (4.3.0)
C [auth R]	1.10.405.10	Mainly Alpha	Orthogonal Bundle	Guanine Nucleotide Dissociation Inhibitor	domain 1	CATH (4.3.0)
B	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01239	Protein prenyltransferase alpha subunit repeat (PPTA)	Protein prenyltransferase alpha subunit repeat	-	Repeat
A	PF07711	Rab geranylgeranyl transferase alpha-subunit, insert domain (RabGGT_insert)	Rab geranylgeranyl transferase alpha-subunit, insert domain	Rab geranylgeranyl transferase (RabGGT) catalyses the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular traff ...	Rab geranylgeranyl transferase (RabGGT) catalyses the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking [1]. This domain is inserted between Pfam:PF01239 repeats. This domain adopts an Ig-like fold and is thought to be involved in protein-protein interactions and might be involved in the recognition and binding of REP [1].	Domain
C [auth R]	PF00996	GDP dissociation inhibitor (GDI)	GDP dissociation inhibitor	-	Family
C [auth R]	PF22603	RAE1/2 domain I, C-terminal region (RAE1_2_domI_C)	RAE1/2 domain I, C-terminal region	This entry represents the C-terminal region of domain I from Rab escort proteins 1/2 (RAE1/2, also known as Rab proteins geranylgeranyltransferase component A 1/2) which are the substrate-binding subunit of the Rab geranylgeranyltransferase (GGTase) ...	This entry represents the C-terminal region of domain I from Rab escort proteins 1/2 (RAE1/2, also known as Rab proteins geranylgeranyltransferase component A 1/2) which are the substrate-binding subunit of the Rab geranylgeranyltransferase (GGTase) complex [1,2]. These proteins bind unprenylated Rab proteins and presents the substrate peptide to the catalytic component B and remains bound to it after the geranylgeranyl transfer reaction.	Domain
B	PF00432	Prenyltransferase and squalene oxidase repeat (Prenyltrans)	Prenyltransferase and squalene oxidase repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT	small GTPase binding protein binding binding enzyme binding GTPase binding catalytic activity, acting on a protein protein geranylgeranyltransferase activity protein prenyltransferase activity Rab geranylgeranyltransferase activity prenyltransferase activity transferase activity catalytic activity transferase activity, transferring alkyl or aryl (other than methyl) groups cation binding small GTPase binding protein binding binding enzyme binding GTPase binding catalytic activity, acting on a protein protein geranylgeranyltransferase activity protein prenyltransferase activity Rab geranylgeranyltransferase activity prenyltransferase activity transferase activity catalytic activity transferase activity, transferring alkyl or aryl (other than methyl) groups cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	macromolecule modification protein prenylation protein geranylgeranylation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process prenylation protein modification process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex polyprenyl diphosphate synthase complex Rab-protein geranylgeranyltransferase complex cytoplasm transferase complex
C [auth R]	Rab Escort Protein 1	small GTPase binding protein binding binding enzyme binding GTPase binding protein-containing complex binding GTPase regulator activity enzyme regulator activity GDP-dissociation inhibitor activity nucleoside-triphosphatase regulator activity molecular function regulator activity enzyme activator activity GTPase activator activity molecular function activator activity	protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport vesicle-mediated transport developmental process multicellular organism development multicellular organismal process anatomical structure development vasculature development blood vessel development system development circulatory system development establishment of protein localization to membrane protein targeting localization within membrane protein localization to membrane protein targeting to membrane macromolecule modification protein prenylation protein geranylgeranylation metabolic process primary metabolic process protein metabolic process macromolecule metabolic process prenylation protein modification process cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication intracellular signaling cassette signal transduction	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex polyprenyl diphosphate synthase complex Rab-protein geranylgeranyltransferase complex transferase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
D [auth P]	AAAA	-	-	-
B	RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT	small GTPase binding protein binding binding enzyme binding GTPase binding isoprenoid binding lipid binding catalytic activity, acting on a protein protein geranylgeranyltransferase activity protein prenyltransferase activity Rab geranylgeranyltransferase activity prenyltransferase activity transferase activity catalytic activity small GTPase binding protein binding binding enzyme binding GTPase binding isoprenoid binding lipid binding catalytic activity, acting on a protein protein geranylgeranyltransferase activity protein prenyltransferase activity Rab geranylgeranyltransferase activity prenyltransferase activity transferase activity catalytic activity transferase activity, transferring alkyl or aryl (other than methyl) groups cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	macromolecule modification protein prenylation protein geranylgeranylation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process prenylation protein modification process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex polyprenyl diphosphate synthase complex Rab-protein geranylgeranyltransferase complex cytoplasm transferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR009087	Rab geranylgeranyltransferase, alpha subunit, insert-domain	Domain
A	IPR002088	Protein prenyltransferase, alpha subunit	Repeat
A	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A	IPR036254	Rab geranylgeranyltransferase, alpha subunit, insert-domain superfamily	Homologous Superfamily
C [auth R]	IPR054420	RAE1/2 domain I, C-terminal region	Domain
C [auth R]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
C [auth R]	IPR001738	Rab protein geranylgeranyltransferase component A	Family
C [auth R]	IPR018203	GDP dissociation inhibitor	Family
B	IPR045089	Prenyltransferase subunit beta	Family
B	IPR026873	Geranylgeranyl transferase type-2 subunit beta	Family
B	IPR001330	PFTB repeat	Repeat
B	IPR008930	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.