1QOL

STRUCTURE OF THE FMDV LEADER PROTEASE

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1qolb_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	FMDV leader protease	FMDV leader protease	(Foot-and-mouth disease virus (strain O1) ) [TaxId: 73482 ],	SCOPe (2.08)
H	d1qolh_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	FMDV leader protease	FMDV leader protease	(Foot-and-mouth disease virus (strain O1) ) [TaxId: 73482 ],	SCOPe (2.08)
A	d1qola_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	FMDV leader protease	FMDV leader protease	(Foot-and-mouth disease virus (strain O1) ) [TaxId: 73482 ],	SCOPe (2.08)
C	d1qolc_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	FMDV leader protease	FMDV leader protease	(Foot-and-mouth disease virus (strain O1) ) [TaxId: 73482 ],	SCOPe (2.08)
D	d1qold_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	FMDV leader protease	FMDV leader protease	(Foot-and-mouth disease virus (strain O1) ) [TaxId: 73482 ],	SCOPe (2.08)
E	d1qole_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	FMDV leader protease	FMDV leader protease	(Foot-and-mouth disease virus (strain O1) ) [TaxId: 73482 ],	SCOPe (2.08)
F	d1qolf_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	FMDV leader protease	FMDV leader protease	(Foot-and-mouth disease virus (strain O1) ) [TaxId: 73482 ],	SCOPe (2.08)
G	d1qolg_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	FMDV leader protease	FMDV leader protease	(Foot-and-mouth disease virus (strain O1) ) [TaxId: 73482 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Cysteine proteinases	8034060	3001808	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Cysteine proteinases	8034060	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8034060	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cysteine proteinases	8034060	3001808	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cysteine proteinases	8034060	3001808	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cysteine proteinases	8034060	3001808	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cysteine proteinases	8034060	3001808	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cysteine proteinases	8034060	3001808	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)
B	Peptidase_C28	e1qolB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C28	ECOD (1.6)
H	Peptidase_C28	e1qolH1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C28	ECOD (1.6)
A	Peptidase_C28	e1qolA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C28	ECOD (1.6)
C	Peptidase_C28	e1qolC1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C28	ECOD (1.6)
D	Peptidase_C28	e1qolD1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C28	ECOD (1.6)
E	Peptidase_C28	e1qolE1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C28	ECOD (1.6)
F	Peptidase_C28	e1qolF1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C28	ECOD (1.6)
G	Peptidase_C28	e1qolG1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C28	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
H	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
D	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
E	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
F	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
G	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF05408	Foot-and-mouth virus L-proteinase (Peptidase_C28)	Foot-and-mouth virus L-proteinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	PROTEASE (NONSTRUCTURAL PROTEIN P20A)	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity endopeptidase activity RNA binding binding organic cyclic compound binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity molecular adaptor activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity structural molecule activity	cellular biosynthetic process cellular 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 cellular biosynthetic process cellular 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 import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transport of virus multicellular organismal process regulation of cellular process response to stimulus negative regulation of biological process modulation by virus of host process negative regulation of cellular metabolic process response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response cytokine production symbiont-mediated perturbation of host innate immune response symbiont-mediated perturbation of host defense response regulation of biological process response to host defenses response to other organism type I interferon production symbiont-mediated perturbation of host immune response negative regulation of metabolic process symbiont-mediated perturbation of host defenses regulation of cellular metabolic process response to external stimulus negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process regulation of metabolic process virus-mediated perturbation of host defense response perturbation by virus of host immune response suppression by virus of host type I interferon production negative regulation of type I interferon production symbiont-mediated perturbation of host process response to host immune response symbiont-mediated suppression of host defenses negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process response to host response to external biotic stimulus modulation of process of another organism negative regulation of macromolecule metabolic process modulation by virus of host cellular process regulation of biosynthetic process suppression by virus of host cytokine production response to defenses of other organism biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression regulation of cellular biosynthetic process negative regulation of biosynthetic process modulation by virus of host cytokine production symbiont-mediated suppression of host cytokine production regulation of type I interferon production transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport regulation of primary metabolic process post-transcriptional regulation of gene expression protein metabolic process regulation of protein metabolic process translation regulation of translation viral gene expression viral protein processing DNA-templated transcription modulation by virus of host chromatin organization cellular component organization chromatin organization cellular component organization or biogenesis virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host symbiont-mediated perturbation of host cellular process catabolic process autophagy positive regulation of biological process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy modulation by virus of host autophagy regulation of catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process proteolysis	membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region viral capsid membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015031	Capsid protein VP4, Picornavirus	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008739	Peptidase C28, foot-and-mouth virus L-proteinase	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000199	Peptidase C3A/C3B, picornaviral	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001676	Picornavirus capsid	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004080	Foot-and-mouth disease virus VP1 coat	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004004	Helicase/polymerase/peptidase polyprotein, Calicivirus-type	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR044067	Picornavirales 3C/3C-like protease domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR033703	Picornavirus/Calicivirus coat protein	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR037080	Capsid protein VP4 superfamily, Picornavirus	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B	L-peptidase M-CSA #746	The leader protease of foot-and-mouth disease virus FMDV Lpro is a papain-like protease where, as well as cleaving itself from the nascent viral polyprotein, disables host cell protein synthesis by specific proteolysis of a cellular protein: the eukaryotic initiation factor 4G (eIF4G). Its sole role in viral maturation is to free itself from the polyprotein by cleavage between its own C-terminus and the N-terminus of VP4 at the sequence ArgLys LeuLys-\|-GlyAlaGlySer. Later it plays the role of lysing the host cell protein eukaryotic initiation factor eIF4G at the sequence AlaAsnLeuGly-\|-ArgThrThrLeu and other eIF4G sequences. As a result, the domain of eIF4G which binds the cap-binding protein eIF4E is separated from the domain of eIF4G which binds eIF3, so that the infected cell is unable to recruit its own capped mRNA to the 40S ribosome. Substrate specificity is achieved with four acidic residues 163-166, not seen in other papain-like proteases.	Defined by 4 residues: ASN:B-18 [auth B-46]ALA:B-23 [auth B-51]HIS:B-120 [auth B-148]ASP:B-135 [auth B-163] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif