1U2R

Crystal Structure of ADP-ribosylated Ribosomal Translocase from Saccharomyces cerevisiae

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1u2ra1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor 2 (eEF-2), domain II	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1u2ra2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor 2 (eEF-2), N-terminal (G) domain	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1u2ra3	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Translational machinery components	Elongation factor 2 (eEF-2), domain IV	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1u2ra5	Alpha and beta proteins (a+b)	Ferredoxin-like	EF-G C-terminal domain-like	EF-G/eEF-2 domains III and V	Elongation factor 2 (eEF-2), C-terminal domain	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1u2ra4	Alpha and beta proteins (a+b)	Ferredoxin-like	EF-G C-terminal domain-like	EF-G/eEF-2 domains III and V	Elongation factor 2 (eEF-2), N-terminal domain	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	EF-G C-terminal domain-like	8043948	3001287	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8043943	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8043945	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-G C-terminal domain-like	8043949	3001287	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043947	3000100	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	GTP_EFTU_D2	e1u2rA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
A	EFG_IV	e1u2rA4	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: EFG_IV	ECOD (1.6)
A	EFG_C	e1u2rA3	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: EFG_C	ECOD (1.6)
A	EFG_II	e1u2rA2	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: EFG_II	ECOD (1.6)
A	MnmE_helical_2nd	e1u2rA5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	3.90.1430.10	Alpha Beta	Alpha-Beta Complex	Yeast translation eEF2 (G' domain)	Yeast translation eEF2 (G' domain)	CATH (4.3.0)
A	3.30.70.870	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Elongation Factor G (Translational Gtpase), domain 3	CATH (4.3.0)
A	3.30.70.240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00679	Elongation factor G C-terminus (EFG_C)	Elongation factor G C-terminus	This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.	Domain
A	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
A	PF14492	Elongation Factor G, domain III (EFG_III)	Elongation Factor G, domain III	This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1].	Domain
A	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain
A	PF03764	Elongation factor G, domain IV (EFG_IV)	Elongation factor G, domain IV	This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Elongation factor 2	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding RNA binding rRNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding guanyl nucleotide binding GTP binding translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding RNA binding rRNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding protein-folding chaperone binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity identical protein binding	regulation of cellular process cellular biosynthetic process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process regulation of nitrogen compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process regulation of translational elongation organic substance metabolic process positive regulation of biosynthetic process regulation of cellular process cellular biosynthetic process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process regulation of nitrogen compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process regulation of translational elongation organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process nitrogen compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of translational elongation biosynthetic process positive regulation of nitrogen compound metabolic process positive regulation of gene expression regulation of translation translational elongation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process maintenance of translational fidelity	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR005517	Translation elongation factor EFG/EF2, domain IV	Domain
A	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A	IPR000640	Elongation factor EFG, domain V-like	Domain
A	IPR031157	Tr-type G domain, conserved site	Conserved Site
A	IPR035647	EF-G domain III/V-like	Homologous Superfamily
A	IPR041095	Elongation Factor G, domain II	Domain
A	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A	IPR005225	Small GTP-binding protein domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	DDE	Parent Component: HIS RESID: AA0040 PSI-MOD : 2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine MOD:00049

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.