5WFI

X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d5wfic_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5wfid_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PLpro Zn-binding domain-like	8091729	3002538	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8091728	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8091730	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8091728	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8091730	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8091728	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLpro Zn-binding domain-like	8091729	3002538	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8091728	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	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	Viral_protease_N	e5wfiA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Viral_protease_N	ECOD (1.6)
A	Viral_protease_C	e5wfiA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
B	Viral_protease_N	e5wfiB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Viral_protease_N	ECOD (1.6)
B	Viral_protease_C	e5wfiB2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
C	ubiquitin_1	e5wfiC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D	ubiquitin_1	e5wfiD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08715	Coronavirus papain-like peptidase (CoV_peptidase)	Coronavirus papain-like peptidase	-	Family
C, D	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	papain-like protease	3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding RNA methyltransferase activity transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides ATP-dependent activity peptidase activity omega peptidase activity catalytic activity, acting on a protein helicase activity RNA helicase activity ATP-dependent activity, acting on RNA endonuclease activity O-methyltransferase activity mRNA (nucleoside-2'-O-)-methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid binding single-stranded RNA binding ubiquitin-like protein peptidase activity cysteine-type deubiquitinase activity deubiquitinase activity cation binding transition metal ion binding zinc ion binding metal ion binding	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host NF-kappaB cascade symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host NF-kappaB cascade modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus viral gene expression viral protein processing modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway gene expression DNA-templated transcription symbiont-mediated degradation of host mRNA symbiont-mediated perturbation of host ubiquitin-like protein modification catabolic process regulation of cellular process autophagy positive regulation of biological process regulation of autophagy positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy regulation of biological process modulation by virus of host autophagy biological regulation regulation of catabolic process positive regulation of catabolic process regulation of metabolic process viral translational frameshifting viral translation proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell cytoplasm part host intracellular organelle host cell perinuclear region of cytoplasm membrane host cell membrane
C, D	Ubiquitin	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development anatomical structure development reproductive structure development system development regulation of mitochondrial membrane potential biological regulation regulation of biological quality regulation of membrane potential catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of biological process neuron apoptotic process regulation of cellular process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process multicellular organismal-level homeostasis homeostatic process energy homeostasis regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule modification post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction intrinsic apoptotic signaling pathway regulation of signaling positive regulation of programmed cell death positive regulation of intracellular signal transduction signal transduction by p53 class mediator positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway positive regulation of signaling cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation brain development diencephalon development forebrain neuron development central nervous system development forebrain neuron differentiation sexual reproduction organelle fission meiotic cell cycle multicellular organismal reproductive process female gamete generation meiotic cell cycle process gamete generation nuclear division organelle organization meiosis I meiosis I cell cycle process female meiosis I female meiotic nuclear division meiotic nuclear division cell cycle cell cycle process positive regulation of protein monoubiquitination protein monoubiquitination regulation of protein monoubiquitination regulation of proteolysis involved in protein catabolic process regulation of proteolysis proteasomal protein catabolic process regulation of catabolic process regulation of proteasomal protein catabolic process regulation of protein catabolic process male meiosis I male meiotic nuclear division male gamete generation connective tissue development adipose tissue development fat pad development tissue development female gonad development female sex differentiation development of primary female sexual characteristics establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated mitochondrion transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cell projection neuron projection plasma membrane bounded cell projection intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle endosome membrane endosome mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane somatodendritic compartment cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
A, B	IPR044384	Non-structural protein 2, MHV-like	Domain
A, B	IPR042515	Non-structural protein NSP15, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A, B	IPR043174	Non-structural protein NSP15, middle domain superfamily	Homologous Superfamily
A, B	IPR044315	Nonstructural protein 14, betacoronavirus	Domain
A, B	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A, B	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
A, B	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A, B	IPR046441	RNA-dependent RNA polymerase, coronavirus	Domain
A, B	IPR044863	Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain	Domain
A, B	IPR044343	Nonstructural protein 13, 1B domain, coronavirus	Domain
A, B	IPR037227	Endoribonuclease EndoU-like	Homologous Superfamily
A, B	IPR027352	Nonstructural protein 13, zinc-binding domain, coronavirus-like	Domain
A, B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B	IPR013016	Peptidase C16, coronavirus	Domain
A, B	IPR009466	Non-structural protein 14, coronavirus	Domain
A, B	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B	IPR046436	Nidovirus 3'-5' exoribonuclease domain	Domain
A, B	IPR047570	NSP12, interface domain, coronavirus	Domain
A, B	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A, B	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
A, B	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A, B	IPR043606	Coronavirus replicase NSP15, N-terminal oligomerization	Domain
A, B	IPR044330	Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus	Domain
A, B	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
A, B	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A, B	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
A, B	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A, B	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B	IPR008740	Peptidase C30, coronavirus	Domain
A, B	IPR044347	RNA-dependent RNA polymerase, coronavirus HKU1-like	Domain
A, B	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A, B	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
A, B	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
A, B	IPR043472	Macro domain-like	Homologous Superfamily
A, B	IPR043609	NendoU domain, nidovirus	Domain
A, B	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
A, B	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A, B	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
A, B	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B	IPR048673	Nonstructural protein 13, stalk domain, coronavirus	Domain
A, B	IPR022570	Betacoronavirus, lineage A, NSP1	Family
A, B	IPR046435	NSP14, guanine-N7-methyltransferase domain, coronavirus	Domain
A, B	IPR009469	RNA-dependent RNA polymerase, N-terminal, coronavirus	Domain
A, B	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A, B	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A, B	IPR048672	Nonstructural protein 13, zinc-binding domain, coronavirus	Domain
A, B	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR043608	Nonstructural protein 15, middle domain, coronavirus	Domain
A, B	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A, B	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
A, B	IPR043610	Non-structural protein 6, coronavirus	Domain
A, B	IPR027351	(+) RNA virus helicase core domain	Domain
A, B	IPR044322	Nonstructural protein 15, middle domain, alpha/betacoronavirus	Domain
A, B	IPR009461	Non-structural protein NSP16, coronavirus-like	Domain
A, B	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A, B	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
A, B	IPR045055	DNA2/NAM7-like helicase	Family
A, B	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A, B	IPR044401	NSP15, NendoU domain, coronavirus	Domain
A, B	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A, B	IPR002705	Peptidase C30/C16, Betacoronavirus	Domain
A, B	IPR044367	Non-structural protein 6, betacoronavirus	Domain
A, B	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A, B	IPR046440	Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain	Domain
A, B	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A, B	IPR046438	Nidovirus 2-O-methyltransferase	Domain
A, B	IPR002589	Macro domain	Domain
A, B	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
A, B	IPR044381	NSP3, DPUP domain, murine hepatitis virus-like	Domain
A, B	IPR044371	Non-structural protein 3, X-domain-like	Domain
A, B	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
C, D	IPR019954	Ubiquitin conserved site	Conserved Site
C, D	IPR050158	Ubiquitin and ubiquitin-like	Family
C, D	IPR000626	Ubiquitin-like domain	Domain
C, D	IPR019956	Ubiquitin domain	Domain
C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily