9RAI | pdb_00009rai

Structure of the S.aureus MecA/ClpC/ClpP degradation system

External Resource: Annotation

Domain Annotation: SCOP2 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)
N [auth G]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
O [auth H]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
P [auth I]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
Q [auth J]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
R [auth K]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
S [auth L]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
T [auth M]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
U [auth N]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
W [auth P]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
Y [auth R]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
Z [auth T]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
X [auth Q]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
V [auth O]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
AA [auth U]	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N], V [auth O], W [auth P], X [auth Q], Y [auth R], Z [auth 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
A, B, C, D, E A, B, C, D, E, F	PF02861	Clp repeat (R) N-terminal domain (Clp_N)	Clp repeat (R) N-terminal domain	-	Family
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N], V [auth O], W [auth P], X [auth Q], Y [auth R], Z [auth T]	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	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins	cellular anatomical structure intracellular anatomical structure cytoplasm endopeptidase Clp complex protein-containing complex catalytic complex
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	ATP-dependent Clp protease ATP-binding subunit ClpC	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	response to copper ion response to stimulus response to metal ion response to chemical response to stress stress response to copper ion stress response to metal ion stress response to cadmium ion response to cadmium ion	-
G [auth S]	unknown substrate	-	-	-
A, B, C, D, E A, B, C, D, E, F	Adapter protein MecA	protein-macromolecule adaptor activity molecular adaptor activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N], V [auth O], W [auth P], X [auth Q], Y [auth R], Z [auth T]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N], V [auth O], W [auth P], X [auth Q], Y [auth R], Z [auth T]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N], V [auth O], W [auth P], X [auth Q], Y [auth R], Z [auth T]	IPR018215	ClpP, Ser active site	Active Site
AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N], V [auth O], W [auth P], X [auth Q], Y [auth R], Z [auth T]	IPR033135	ClpP, histidine active site	Active Site
AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], AA [auth U], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N], V [auth O], W [auth P], X [auth Q], Y [auth R], Z [auth T]	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR001270	ClpA/B family	Family
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR018368	ClpA/B, conserved site 1	Conserved Site
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR041546	ClpA/ClpB, AAA lid domain	Domain
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR004176	Clp, repeat (R) N-terminal domain	Domain
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR050130	ATP-dependent Clp protease/Chaperone ClpA/ClpB	Family
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR028299	ClpA/B, conserved site 2	Conserved Site
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR003593	AAA+ ATPase domain	Domain
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR003959	ATPase, AAA-type, core	Domain
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR001943	UVR domain	Domain
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR019489	Clp ATPase, C-terminal	Domain
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR036628	Clp, N-terminal domain superfamily	Homologous Superfamily
H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], H [auth a], I [auth b], J [auth c], K [auth d], L [auth e], M [auth f]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008681	Negative regulator of genetic competence, MecA	Family
A, B, C, D, E A, B, C, D, E, F	IPR038471	MecA, C-terminal domain superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.