Annotations: 8YD0

CryoEM structure of M. tuberculosis ClpXP1P2 complex bound to bortezomib

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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)
S [auth U]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
R [auth T]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
Q [auth S]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
P [auth R]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
O [auth Q]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
N [auth P]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
M [auth O]	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
T [auth V]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
L [auth N]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
K [auth M]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
H [auth I]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	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)
S [auth U]	UCR_hinge	e8yd0U1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
R [auth T]	UCR_hinge	e8yd0T1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
Q [auth S]	UCR_hinge	e8yd0S1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
P [auth R]	UCR_hinge	e8yd0R1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
O [auth Q]	UCR_hinge	e8yd0Q1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
N [auth P]	UCR_hinge	e8yd0P1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
M [auth O]	UCR_hinge	e8yd0O1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
T [auth V]	UCR_hinge	e8yd0V1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
L [auth N]	UCR_hinge	e8yd0N1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
K [auth M]	UCR_hinge	e8yd0M1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
J [auth L]	UCR_hinge	e8yd0L1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
I [auth K]	UCR_hinge	e8yd0K1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
H [auth I]	UCR_hinge	e8yd0I1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
G [auth H]	LRR_1, LRR_5, LRR_6, LRR_8	e8yd0H01	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: LRR_1, LRR_5, LRR_6, LRR_8	ECOD (v295.2)
F	UCR_hinge	e8yd0F1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
E	UCR_hinge	e8yd0E1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
D	UCR_hinge	e8yd0D1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
C	UCR_hinge	e8yd0C1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
B	UCR_hinge	e8yd0B1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
A	LRR_1, LRR_5, LRR_6, LRR_8	e8yd0A01	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: LRR_1, LRR_5, LRR_6, LRR_8	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U]	PF00574	Clp protease (CLP_protease)	Clp protease	The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large in ...	The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion.	Domain
G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], T [auth V]	PF00574	Clp protease (CLP_protease)	Clp protease	The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large in ...	The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion.	Domain
A, B, C, D, E A, B, C, D, E, F	PF10431	C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small)	C-terminal, D2-small domain, of ClpB protein	This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 ...	This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly [1]. The domain is associated with two Clp_N, Pfam:PF02861, at the N-terminus as well as AAA, Pfam:PF00004 and AAA_2, Pfam:PF07724.	Domain
A, B, C, D, E A, B, C, D, E, F	PF07724	AAA domain (Cdc48 subfamily) (AAA_2)	AAA domain (Cdc48 subfamily)	This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U]	ATP-dependent Clp protease proteolytic subunit 1	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity ATP-dependent peptidase activity ATP-dependent activity ATPase binding protein binding binding enzyme binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process catabolic process protein catabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm
G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], T [auth V]	ATP-dependent Clp protease proteolytic subunit 2	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity ATP-dependent peptidase activity ATP-dependent activity ATPase binding protein binding binding enzyme binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process catabolic process protein catabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm
A, B, C, D, E A, B, C, D, E, F	ATP-dependent Clp protease ATP-binding subunit ClpX	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 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 ATP hydrolysis 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 ATP-dependent activity cation binding transition metal ion binding zinc ion binding metal ion binding protein binding protein dimerization activity ATP-dependent protein folding chaperone protein folding chaperone	cellular process cell division protein polymerization regulation of biological process regulation of cellular process regulation of cellular component organization negative regulation of cellular component organization protein-containing complex organization biological regulation negative regulation of biological process regulation of cellular component biogenesis negative regulation of protein-containing complex assembly cellular component organization cellular component biogenesis cellular process cell division protein polymerization regulation of biological process regulation of cellular process regulation of cellular component organization negative regulation of cellular component organization protein-containing complex organization biological regulation negative regulation of biological process regulation of cellular component biogenesis negative regulation of protein-containing complex assembly cellular component organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly regulation of protein polymerization protein-containing complex assembly negative regulation of cellular process negative regulation of protein polymerization cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure catalytic complex peptidase complex cytosolic proteasome complex HslUV protease complex cellular anatomical structure proteasome complex endopeptidase complex cytoplasm cytosol intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U]	IPR033135	ClpP, histidine active site	Active Site
M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], M [auth O], N [auth P], O [auth Q], P [auth R], Q [auth S], R [auth T], S [auth U]	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], T [auth V]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], T [auth V]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], T [auth V]	IPR018215	ClpP, Ser active site	Active Site
G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], T [auth V]	IPR033135	ClpP, histidine active site	Active Site
G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], G [auth H], H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], T [auth V]	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
A, B, C, D, E A, B, C, D, E, F	IPR050052	ATP-dependent Clp protease ATP-binding subunit ClpX	Family
A, B, C, D, E A, B, C, D, E, F	IPR046425	Clp protease, ATP-binding subunit ClpX, bacteria	Family
A, B, C, D, E A, B, C, D, E, F	IPR004487	Clp protease, ATP-binding subunit ClpX	Family
A, B, C, D, E A, B, C, D, E, F	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR059188	ClpX-like, zinc ribbon domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR010603	ATP-dependent Clp protease ATP-binding subunit ClpX, zinc ribbon domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003959	ATPase, AAA-type, core	Domain
A, B, C, D, E A, B, C, D, E, F	IPR019489	Clp ATPase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR038366	Zinc finger, ClpX C4-type superfamily	Homologous Superfamily