Annotations: 8YD1

CryoEM structure of M. tuberculosis ClpC1P1P2 complex bound to bortezomib, conformation 1

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)
P	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	ClpP/crotonase	8038635	3000033	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	ClpP/crotonase	8068493	3000033	SCOP2B (2022-06-29)
J	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)
P	UCR_hinge	e8yd1P1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
Q	UCR_hinge	e8yd1Q1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
T	UCR_hinge	e8yd1T1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
S	UCR_hinge	e8yd1S1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
R	UCR_hinge	e8yd1R1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
O	UCR_hinge	e8yd1O1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
N	UCR_hinge	e8yd1N1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
G	LRR_1, LRR_5, LRR_6, LRR_8	e8yd1G01	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)
H	UCR_hinge	e8yd1H1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
I	UCR_hinge	e8yd1I1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
L	UCR_hinge	e8yd1L1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
M	UCR_hinge	e8yd1M1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
K	UCR_hinge	e8yd1K1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
J	UCR_hinge	e8yd1J1	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	e8yd1B1	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	e8yd1C1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
F	UCR_hinge	e8yd1F1	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	e8yd1E1	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	e8yd1D1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)
A	UCR_hinge	e8yd1A1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: UCR_hinge	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
N, O, P, Q, R N, O, P, Q, R, S, T	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, H, I, J, K G, H, I, J, K, L, M	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	PF17871	AAA lid domain (AAA_lid_9)	AAA lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain
A, B, C, D, E A, B, C, D, E, F	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
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
U [auth a]	Beta-casein	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity cysteine-type endopeptidase inhibitor activity peptidase inhibitor activity endopeptidase regulator activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity cysteine-type endopeptidase inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity identical protein binding protein binding protein homodimerization activity protein dimerization activity potassium channel regulator activity channel regulator activity transporter inhibitor activity ion channel inhibitor activity ion channel regulator activity potassium channel inhibitor activity transporter regulator activity channel inhibitor activity	response to ketone response to stimulus response to lipid response to alcohol response to chemical response to oxygen-containing compound response to dehydroepiandrosterone regulation of localization regulation of body fluid levels multicellular organismal process negative regulation of lactation regulation of developmental process transport mammary gland development response to ketone response to stimulus response to lipid response to alcohol response to chemical response to oxygen-containing compound response to dehydroepiandrosterone regulation of localization regulation of body fluid levels multicellular organismal process negative regulation of lactation regulation of developmental process transport mammary gland development negative regulation of biological process gland development negative regulation of transport localization multicellular organism development negative regulation of secretion anatomical structure development lactation regulation of multicellular organismal process regulation of biological quality developmental process regulation of biological process regulation of multicellular organismal development regulation of transport secretion negative regulation of developmental process biological regulation animal organ development establishment of localization regulation of secretion body fluid secretion regulation of lactation negative regulation of multicellular organismal process animal gross anatomical part developmental process response to hormone response to steroid hormone response to endogenous stimulus response to progesterone cellular response to stimulus regulation of cellular process signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response response to external stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response response to heat response to abiotic stimulus response to temperature stimulus response to cytokine cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway negative regulation of tumor necrosis factor-mediated signaling pathway response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus negative regulation of cytokine-mediated signaling pathway response to tumor necrosis factor response to 11-deoxycorticosterone response to mineralocorticoid response to corticosteroid response to estradiol	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm extracellular region
N, O, P, Q, R N, O, P, Q, R, S, T	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, H, I, J, K G, H, I, J, K, L, M	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 ClpC1	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 identical protein binding protein binding protein homodimerization activity protein dimerization activity 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 protein folding chaperone	-	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
U [auth a]	IPR001588	Casein, alpha/beta	Family
U [auth a]	IPR016345	Casein, beta	Family
U [auth a]	IPR031305	Casein alpha/beta, conserved site	Conserved Site
N, O, P, Q, R N, O, P, Q, R, S, T	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
N, O, P, Q, R N, O, P, Q, R, S, T	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
N, O, P, Q, R N, O, P, Q, R, S, T	IPR033135	ClpP, histidine active site	Active Site
N, O, P, Q, R N, O, P, Q, R, S, T	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
G, H, I, J, K G, H, I, J, K, L, M	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L, M	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
G, H, I, J, K G, H, I, J, K, L, M	IPR018215	ClpP, Ser active site	Active Site
G, H, I, J, K G, H, I, J, K, L, M	IPR033135	ClpP, histidine active site	Active Site
G, H, I, J, K G, H, I, J, K, L, M	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
A, B, C, D, E A, B, C, D, E, F	IPR001270	ClpA/B family	Family
A, B, C, D, E A, B, C, D, E, F	IPR018368	ClpA/B, conserved site 1	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR041546	ClpA/ClpB, AAA lid domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004176	Clp, repeat (R) N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050130	ATP-dependent Clp protease/Chaperone ClpA/ClpB	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	IPR003959	ATPase, AAA-type, core	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001943	UVR domain	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	IPR036628	Clp, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily