1G4B

CRYSTAL STRUCTURES OF THE HSLVU PEPTIDASE-ATPASE COMPLEX REVEAL AN ATP-DEPENDENT PROTEOLYSIS MECHANISM

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth E]	d1g4be_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	HslU	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth F]	d1g4bf_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	HslU	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth K]	d1g4bk_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	HslU	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth L]	d1g4bl_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	HslU	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth M]	d1g4bm_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth N]	d1g4bn_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G [auth O]	d1g4bo_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H [auth P]	d1g4bp_	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Proteasome subunits	HslV (ClpQ) protease	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth E]	SCOP2B Superfamily	RecA-like P-loop NTPases	8044319	3002019	SCOP2B (2022-06-29)
B [auth F]	SCOP2B Superfamily	RecA-like P-loop NTPases	8044319	3002019	SCOP2B (2022-06-29)
C [auth K]	SCOP2B Superfamily	RecA-like P-loop NTPases	8044319	3002019	SCOP2B (2022-06-29)
D [auth L]	SCOP2B Superfamily	RecA-like P-loop NTPases	8044319	3002019	SCOP2B (2022-06-29)
E [auth M]	SCOP2B Superfamily	Class II glutamine amidotransferases	8036886	3000131	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	Class II glutamine amidotransferases	8036886	3000131	SCOP2B (2022-06-29)
G [auth O]	SCOP2B Superfamily	Class II glutamine amidotransferases	8036886	3000131	SCOP2B (2022-06-29)
H [auth P]	SCOP2B Superfamily	Class II glutamine amidotransferases	8036886	3000131	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 [auth E]	ClpB_D2-small	e1g4bE2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: ClpB_D2-small	ECOD (1.6)
A [auth E]	Sigma54_activat	e1g4bE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
B [auth F]	ClpB_D2-small	e1g4bF2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: ClpB_D2-small	ECOD (1.6)
B [auth F]	Sigma54_activat	e1g4bF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
C [auth K]	ClpB_D2-small	e1g4bK2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: ClpB_D2-small	ECOD (1.6)
C [auth K]	Sigma54_activat	e1g4bK1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
D [auth L]	ClpB_D2-small	e1g4bL2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: ClpB_D2-small	ECOD (1.6)
D [auth L]	Sigma54_activat	e1g4bL1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
E [auth M]	Proteasome	e1g4bM1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
F [auth N]	Proteasome	e1g4bN1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
G [auth O]	Proteasome	e1g4bO1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)
H [auth P]	Proteasome	e1g4bP1	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Proteasome subunits	F: Proteasome	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], B [auth F], C [auth K], D [auth L]	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	Domain
E [auth M], F [auth N], G [auth O], H [auth P]	PF00227	Proteasome subunit (Proteasome)	Proteasome subunit	The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity ...	The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes [1]. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria [1]. The second is call beta-proteobacteria proteasome homologue (BPH) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], B [auth F], C [auth K], D [auth L]	ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding protein binding protein domain specific binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic 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 identical protein binding proteasome-activating activity	cellular process protein unfolding cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus protein denaturation catabolic process metabolic process primary metabolic process cellular process protein unfolding cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus protein denaturation catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process proteolysis involved in protein catabolic process proteolysis	membrane cellular anatomical entity protein-containing complex intracellular anatomical structure catalytic complex peptidase complex cytosolic proteasome complex HslUV protease complex proteasome complex endopeptidase complex cytoplasm cytosol intracellular protein-containing complex
E [auth M], F [auth N], G [auth O], H [auth P]	ATP-DEPENDENT PROTEASE HSLV	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding protein binding protein domain specific binding peptidase activity catalytic activity, acting on a protein threonine-type peptidase activity hydrolase activity catalytic activity endopeptidase activity threonine-type endopeptidase activity identical protein binding	cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus cellular process response to temperature stimulus protein denaturation catabolic process metabolic process primary metabolic process protein catabolic process cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus cellular process response to temperature stimulus protein denaturation catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process proteolysis involved in protein catabolic process proteolysis	protein-containing complex intracellular anatomical structure catalytic complex peptidase complex cellular anatomical entity cytosolic proteasome complex HslUV protease complex proteasome complex endopeptidase complex cytoplasm cytosol intracellular protein-containing complex proteasome core complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], B [auth F], C [auth K], D [auth L]	IPR050052	ATP-dependent Clp protease ATP-binding subunit ClpX	Family
A [auth E], B [auth F], C [auth K], D [auth L]	IPR003593	AAA+ ATPase domain	Domain
A [auth E], B [auth F], C [auth K], D [auth L]	IPR003959	ATPase, AAA-type, core	Domain
A [auth E], B [auth F], C [auth K], D [auth L]	IPR004491	Heat shock protein HslU	Family
A [auth E], B [auth F], C [auth K], D [auth L]	IPR019489	Clp ATPase, C-terminal	Domain
A [auth E], B [auth F], C [auth K], D [auth L]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E [auth M], F [auth N], G [auth O], H [auth P]	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
E [auth M], F [auth N], G [auth O], H [auth P]	IPR023333	Proteasome B-type subunit	Family
E [auth M], F [auth N], G [auth O], H [auth P]	IPR001353	Proteasome, subunit alpha/beta	Family
E [auth M], F [auth N], G [auth O], H [auth P]	IPR022281	ATP-dependent protease, HslV subunit	Family

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.