Annotations: 9C87

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX

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)
U [auth v]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
T [auth u]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
S [auth t]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
R [auth s]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
Q [auth r]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
P [auth q]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
O [auth p]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
N [auth n]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
M [auth m]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
L [auth l]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
K [auth k]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
J [auth j]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
I [auth i]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
H [auth h]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
G [auth S]	SCOP2B Superfamily	Dihydrofolate reductase-like	8032695	3001255	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)
F	WD40	e9c87F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
E	WD40	e9c87E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
D	WD40	e9c87D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
C	WD40	e9c87C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
B	WD40	e9c87B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
A	PRODH	e9c87A01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PRODH	ECOD (v294.2)
U [auth v]	WD40	e9c87v1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
T [auth u]	WD40	e9c87u1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
S [auth t]	WD40	e9c87t1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
R [auth s]	WD40	e9c87s1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
Q [auth r]	WD40	e9c87r1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
P [auth q]	WD40	e9c87q1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
O [auth p]	WD40	e9c87p1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
N [auth n]	WD40	e9c87n1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
M [auth m]	WD40	e9c87m1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
L [auth l]	WD40	e9c87l1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
K [auth k]	WD40	e9c87k1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
J [auth j]	WD40	e9c87j1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
I [auth i]	WD40	e9c87i1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
H [auth h]	WD40	e9c87h1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
G [auth S]	PRODH	e9c87S01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PRODH	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
G [auth S]	PF00186	Dihydrofolate reductase (DHFR_1)	Dihydrofolate reductase		Domain
G [auth S]	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

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	ATP-dependent Clp protease ATP-binding subunit ClpX	protein binding binding enzyme binding protease binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding protein binding binding enzyme binding protease binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity 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 cation binding transition metal ion binding zinc ion binding metal ion binding ATP-dependent peptidase activity peptidase activity catalytic activity, acting on a protein protein dimerization activity disordered domain specific binding protein domain specific binding identical protein binding	cellular process cell division protein unfolding	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
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	ATP-dependent Clp protease proteolytic subunit	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 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 identical protein binding	regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation positive regulation of biological process cellular process regulation of programmed cell death cell death programmed cell death positive regulation of cellular process catabolic process proteasomal protein catabolic process metabolic process primary metabolic process regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation positive regulation of biological process cellular process regulation of programmed cell death cell death programmed cell death positive regulation of cellular process catabolic process proteasomal protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process response to stimulus response to radiation response to abiotic stimulus response to stress response to heat response to temperature stimulus protein quality control for misfolded or incompletely synthesized proteins	cellular anatomical structure membrane 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 endopeptidase Clp complex
G [auth S]	Dihydrofolate reductase	organic acid binding binding ion binding anion binding carboxylic acid binding heterocyclic compound binding methotrexate binding small molecule binding NADP+ binding nucleotide binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding NADP binding organic acid binding binding ion binding anion binding carboxylic acid binding heterocyclic compound binding methotrexate binding small molecule binding NADP+ binding nucleotide binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding NADP binding dihydrofolic acid binding modified amino acid binding NADPH binding vitamin binding folic acid binding dihydrofolate reductase activity oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors catalytic activity	response to stimulus response to chemical response to xenobiotic stimulus response to methotrexate response to oxygen-containing compound response to nitrogen compound small molecule metabolic process metabolic process cellular process one-carbon metabolic process oxoacid metabolic process folic acid-containing compound metabolic process dicarboxylic acid metabolic process dihydrofolate metabolic process response to stimulus response to chemical response to xenobiotic stimulus response to methotrexate response to oxygen-containing compound response to nitrogen compound small molecule metabolic process metabolic process cellular process one-carbon metabolic process oxoacid metabolic process folic acid-containing compound metabolic process dicarboxylic acid metabolic process dihydrofolate metabolic process carboxylic acid metabolic process modified amino acid metabolic process pteridine-containing compound metabolic process folic acid metabolic process response to antibiotic folic acid biosynthetic process folic acid-containing compound biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process modified amino acid biosynthetic process vitamin biosynthetic process vitamin metabolic process carboxylic acid biosynthetic process biosynthetic process pteridine-containing compound biosynthetic process dicarboxylic acid biosynthetic process tetrahydrofolate biosynthetic process tetrahydrofolate metabolic process 10-formyltetrahydrofolate metabolic process 10-formyltetrahydrofolate biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	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	IPR050052	ATP-dependent Clp protease ATP-binding subunit ClpX	Family
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	IPR038366	Zinc finger, ClpX C4-type superfamily	Homologous Superfamily
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR018215	ClpP, Ser active site	Active Site
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR033135	ClpP, histidine active site	Active Site
G [auth S]	IPR017925	Dihydrofolate reductase conserved site	Conserved Site
G [auth S]	IPR012259	Dihydrofolate reductase	Family
G [auth S]	IPR024072	Dihydrofolate reductase-like domain superfamily	Homologous Superfamily
G [auth S]	IPR001796	Dihydrofolate reductase domain	Domain