8QHC | pdb_00008qhc

Cryo-EM structure of SidH from Legionella pneumophila in complex with LubX

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth C]	SCOP2B Superfamily	Ras-like P-loop GTPases	8056530	3002022	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056533	3002024	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056531	3002024	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF04564	U-box domain (U-box)	U-box domain	The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop ...	The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process [1-3]. This domain is related to the Ring finger Pfam:PF00097 but lacks the zinc binding residues [4].	Domain
A [auth C]	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 [auth C]	PF03143	Elongation factor Tu C-terminal domain (GTP_EFTU_D3)	Elongation factor Tu C-terminal domain	Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts Pfam:PF00889 [2].	Domain
A [auth C]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	E3 ubiquitin--protein ligase	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity protein binding binding protein-folding chaperone binding	regulation of biological process regulation of cellular process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of proteolysis proteolysis positive regulation of proteolysis metabolic process regulation of biological process regulation of cellular process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of proteolysis proteolysis positive regulation of proteolysis metabolic process cellular process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein cellular response to stress response to stimulus response to stress response to topologically incorrect protein catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process protein quality control for misfolded or incompletely synthesized proteins proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process	host cellular component cellular anatomical structure host cell other organism part extracellular region intracellular anatomical structure cytoplasm
C [auth A]	Protein SidH	-	-	-
B	t-RNA	-	-	-
A [auth C]	Elongation factor Tu	guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding translation factor activity translation elongation factor activity RNA binding nucleic acid binding GTP binding purine ribonucleoside triphosphate 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	response to stimulus response to chemical response to antibiotic primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR003613	U-box domain	Domain
D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth C]	IPR005225	Small GTP-binding domain	Domain
A [auth C]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A [auth C]	IPR033720	Elongation factor Tu, domain 2	Domain
A [auth C]	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A [auth C]	IPR031157	Tr-type G domain, conserved site	Conserved Site
A [auth C]	IPR004541	Translation elongation factor EFTu/EF1A, bacterial/organelle	Family
A [auth C]	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A [auth C]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A [auth C]	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
A [auth C]	IPR050055	Elongation factor Tu GTPase	Family
A [auth C]	IPR041709	Elongation factor Tu (EF-Tu), GTP-binding domain	Domain
A [auth C]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.