8E8Q

Cryo-EM structure of substrate-free DNClpX.ClpP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005524	molecular_function	ATP binding
A	0006457	biological_process	protein folding
A	0016887	molecular_function	ATP hydrolysis activity
A	0051082	molecular_function	unfolded protein binding
A	0140662	molecular_function	ATP-dependent protein folding chaperone
B	0005524	molecular_function	ATP binding
B	0006457	biological_process	protein folding
B	0016887	molecular_function	ATP hydrolysis activity
B	0051082	molecular_function	unfolded protein binding
B	0140662	molecular_function	ATP-dependent protein folding chaperone
C	0005524	molecular_function	ATP binding
C	0006457	biological_process	protein folding
C	0016887	molecular_function	ATP hydrolysis activity
C	0051082	molecular_function	unfolded protein binding
C	0140662	molecular_function	ATP-dependent protein folding chaperone
D	0005524	molecular_function	ATP binding
D	0006457	biological_process	protein folding
D	0016887	molecular_function	ATP hydrolysis activity
D	0051082	molecular_function	unfolded protein binding
D	0140662	molecular_function	ATP-dependent protein folding chaperone
E	0005524	molecular_function	ATP binding
E	0006457	biological_process	protein folding
E	0016887	molecular_function	ATP hydrolysis activity
E	0051082	molecular_function	unfolded protein binding
E	0140662	molecular_function	ATP-dependent protein folding chaperone
F	0005524	molecular_function	ATP binding
F	0006457	biological_process	protein folding
F	0016887	molecular_function	ATP hydrolysis activity
F	0051082	molecular_function	unfolded protein binding
F	0140662	molecular_function	ATP-dependent protein folding chaperone
H	0004176	molecular_function	ATP-dependent peptidase activity
H	0004252	molecular_function	serine-type endopeptidase activity
H	0005515	molecular_function	protein binding
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006508	biological_process	proteolysis
H	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
H	0008233	molecular_function	peptidase activity
H	0008236	molecular_function	serine-type peptidase activity
H	0009266	biological_process	response to temperature stimulus
H	0009314	biological_process	response to radiation
H	0009368	cellular_component	endopeptidase Clp complex
H	0009376	cellular_component	HslUV protease complex
H	0009408	biological_process	response to heat
H	0010498	biological_process	proteasomal protein catabolic process
H	0016020	cellular_component	membrane
H	0016787	molecular_function	hydrolase activity
H	0042802	molecular_function	identical protein binding
H	0043068	biological_process	positive regulation of programmed cell death
H	0051117	molecular_function	ATPase binding
I	0004176	molecular_function	ATP-dependent peptidase activity
I	0004252	molecular_function	serine-type endopeptidase activity
I	0005515	molecular_function	protein binding
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0006508	biological_process	proteolysis
I	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
I	0008233	molecular_function	peptidase activity
I	0008236	molecular_function	serine-type peptidase activity
I	0009266	biological_process	response to temperature stimulus
I	0009314	biological_process	response to radiation
I	0009368	cellular_component	endopeptidase Clp complex
I	0009376	cellular_component	HslUV protease complex
I	0009408	biological_process	response to heat
I	0010498	biological_process	proteasomal protein catabolic process
I	0016020	cellular_component	membrane
I	0016787	molecular_function	hydrolase activity
I	0042802	molecular_function	identical protein binding
I	0043068	biological_process	positive regulation of programmed cell death
I	0051117	molecular_function	ATPase binding
J	0004176	molecular_function	ATP-dependent peptidase activity
J	0004252	molecular_function	serine-type endopeptidase activity
J	0005515	molecular_function	protein binding
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0006508	biological_process	proteolysis
J	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
J	0008233	molecular_function	peptidase activity
J	0008236	molecular_function	serine-type peptidase activity
J	0009266	biological_process	response to temperature stimulus
J	0009314	biological_process	response to radiation
J	0009368	cellular_component	endopeptidase Clp complex
J	0009376	cellular_component	HslUV protease complex
J	0009408	biological_process	response to heat
J	0010498	biological_process	proteasomal protein catabolic process
J	0016020	cellular_component	membrane
J	0016787	molecular_function	hydrolase activity
J	0042802	molecular_function	identical protein binding
J	0043068	biological_process	positive regulation of programmed cell death
J	0051117	molecular_function	ATPase binding
K	0004176	molecular_function	ATP-dependent peptidase activity
K	0004252	molecular_function	serine-type endopeptidase activity
K	0005515	molecular_function	protein binding
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0006508	biological_process	proteolysis
K	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
K	0008233	molecular_function	peptidase activity
K	0008236	molecular_function	serine-type peptidase activity
K	0009266	biological_process	response to temperature stimulus
K	0009314	biological_process	response to radiation
K	0009368	cellular_component	endopeptidase Clp complex
K	0009376	cellular_component	HslUV protease complex
K	0009408	biological_process	response to heat
K	0010498	biological_process	proteasomal protein catabolic process
K	0016020	cellular_component	membrane
K	0016787	molecular_function	hydrolase activity
K	0042802	molecular_function	identical protein binding
K	0043068	biological_process	positive regulation of programmed cell death
K	0051117	molecular_function	ATPase binding
L	0004176	molecular_function	ATP-dependent peptidase activity
L	0004252	molecular_function	serine-type endopeptidase activity
L	0005515	molecular_function	protein binding
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0006508	biological_process	proteolysis
L	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
L	0008233	molecular_function	peptidase activity
L	0008236	molecular_function	serine-type peptidase activity
L	0009266	biological_process	response to temperature stimulus
L	0009314	biological_process	response to radiation
L	0009368	cellular_component	endopeptidase Clp complex
L	0009376	cellular_component	HslUV protease complex
L	0009408	biological_process	response to heat
L	0010498	biological_process	proteasomal protein catabolic process
L	0016020	cellular_component	membrane
L	0016787	molecular_function	hydrolase activity
L	0042802	molecular_function	identical protein binding
L	0043068	biological_process	positive regulation of programmed cell death
L	0051117	molecular_function	ATPase binding
M	0004176	molecular_function	ATP-dependent peptidase activity
M	0004252	molecular_function	serine-type endopeptidase activity
M	0005515	molecular_function	protein binding
M	0005737	cellular_component	cytoplasm
M	0005829	cellular_component	cytosol
M	0006508	biological_process	proteolysis
M	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
M	0008233	molecular_function	peptidase activity
M	0008236	molecular_function	serine-type peptidase activity
M	0009266	biological_process	response to temperature stimulus
M	0009314	biological_process	response to radiation
M	0009368	cellular_component	endopeptidase Clp complex
M	0009376	cellular_component	HslUV protease complex
M	0009408	biological_process	response to heat
M	0010498	biological_process	proteasomal protein catabolic process
M	0016020	cellular_component	membrane
M	0016787	molecular_function	hydrolase activity
M	0042802	molecular_function	identical protein binding
M	0043068	biological_process	positive regulation of programmed cell death
M	0051117	molecular_function	ATPase binding
N	0004176	molecular_function	ATP-dependent peptidase activity
N	0004252	molecular_function	serine-type endopeptidase activity
N	0005515	molecular_function	protein binding
N	0005737	cellular_component	cytoplasm
N	0005829	cellular_component	cytosol
N	0006508	biological_process	proteolysis
N	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
N	0008233	molecular_function	peptidase activity
N	0008236	molecular_function	serine-type peptidase activity
N	0009266	biological_process	response to temperature stimulus
N	0009314	biological_process	response to radiation
N	0009368	cellular_component	endopeptidase Clp complex
N	0009376	cellular_component	HslUV protease complex
N	0009408	biological_process	response to heat
N	0010498	biological_process	proteasomal protein catabolic process
N	0016020	cellular_component	membrane
N	0016787	molecular_function	hydrolase activity
N	0042802	molecular_function	identical protein binding
N	0043068	biological_process	positive regulation of programmed cell death
N	0051117	molecular_function	ATPase binding
h	0004176	molecular_function	ATP-dependent peptidase activity
h	0004252	molecular_function	serine-type endopeptidase activity
h	0005515	molecular_function	protein binding
h	0005737	cellular_component	cytoplasm
h	0005829	cellular_component	cytosol
h	0006508	biological_process	proteolysis
h	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
h	0008233	molecular_function	peptidase activity
h	0008236	molecular_function	serine-type peptidase activity
h	0009266	biological_process	response to temperature stimulus
h	0009314	biological_process	response to radiation
h	0009368	cellular_component	endopeptidase Clp complex
h	0009376	cellular_component	HslUV protease complex
h	0009408	biological_process	response to heat
h	0010498	biological_process	proteasomal protein catabolic process
h	0016020	cellular_component	membrane
h	0016787	molecular_function	hydrolase activity
h	0042802	molecular_function	identical protein binding
h	0043068	biological_process	positive regulation of programmed cell death
h	0051117	molecular_function	ATPase binding
i	0004176	molecular_function	ATP-dependent peptidase activity
i	0004252	molecular_function	serine-type endopeptidase activity
i	0005515	molecular_function	protein binding
i	0005737	cellular_component	cytoplasm
i	0005829	cellular_component	cytosol
i	0006508	biological_process	proteolysis
i	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
i	0008233	molecular_function	peptidase activity
i	0008236	molecular_function	serine-type peptidase activity
i	0009266	biological_process	response to temperature stimulus
i	0009314	biological_process	response to radiation
i	0009368	cellular_component	endopeptidase Clp complex
i	0009376	cellular_component	HslUV protease complex
i	0009408	biological_process	response to heat
i	0010498	biological_process	proteasomal protein catabolic process
i	0016020	cellular_component	membrane
i	0016787	molecular_function	hydrolase activity
i	0042802	molecular_function	identical protein binding
i	0043068	biological_process	positive regulation of programmed cell death
i	0051117	molecular_function	ATPase binding
j	0004176	molecular_function	ATP-dependent peptidase activity
j	0004252	molecular_function	serine-type endopeptidase activity
j	0005515	molecular_function	protein binding
j	0005737	cellular_component	cytoplasm
j	0005829	cellular_component	cytosol
j	0006508	biological_process	proteolysis
j	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
j	0008233	molecular_function	peptidase activity
j	0008236	molecular_function	serine-type peptidase activity
j	0009266	biological_process	response to temperature stimulus
j	0009314	biological_process	response to radiation
j	0009368	cellular_component	endopeptidase Clp complex
j	0009376	cellular_component	HslUV protease complex
j	0009408	biological_process	response to heat
j	0010498	biological_process	proteasomal protein catabolic process
j	0016020	cellular_component	membrane
j	0016787	molecular_function	hydrolase activity
j	0042802	molecular_function	identical protein binding
j	0043068	biological_process	positive regulation of programmed cell death
j	0051117	molecular_function	ATPase binding
k	0004176	molecular_function	ATP-dependent peptidase activity
k	0004252	molecular_function	serine-type endopeptidase activity
k	0005515	molecular_function	protein binding
k	0005737	cellular_component	cytoplasm
k	0005829	cellular_component	cytosol
k	0006508	biological_process	proteolysis
k	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
k	0008233	molecular_function	peptidase activity
k	0008236	molecular_function	serine-type peptidase activity
k	0009266	biological_process	response to temperature stimulus
k	0009314	biological_process	response to radiation
k	0009368	cellular_component	endopeptidase Clp complex
k	0009376	cellular_component	HslUV protease complex
k	0009408	biological_process	response to heat
k	0010498	biological_process	proteasomal protein catabolic process
k	0016020	cellular_component	membrane
k	0016787	molecular_function	hydrolase activity
k	0042802	molecular_function	identical protein binding
k	0043068	biological_process	positive regulation of programmed cell death
k	0051117	molecular_function	ATPase binding
l	0004176	molecular_function	ATP-dependent peptidase activity
l	0004252	molecular_function	serine-type endopeptidase activity
l	0005515	molecular_function	protein binding
l	0005737	cellular_component	cytoplasm
l	0005829	cellular_component	cytosol
l	0006508	biological_process	proteolysis
l	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
l	0008233	molecular_function	peptidase activity
l	0008236	molecular_function	serine-type peptidase activity
l	0009266	biological_process	response to temperature stimulus
l	0009314	biological_process	response to radiation
l	0009368	cellular_component	endopeptidase Clp complex
l	0009376	cellular_component	HslUV protease complex
l	0009408	biological_process	response to heat
l	0010498	biological_process	proteasomal protein catabolic process
l	0016020	cellular_component	membrane
l	0016787	molecular_function	hydrolase activity
l	0042802	molecular_function	identical protein binding
l	0043068	biological_process	positive regulation of programmed cell death
l	0051117	molecular_function	ATPase binding
m	0004176	molecular_function	ATP-dependent peptidase activity
m	0004252	molecular_function	serine-type endopeptidase activity
m	0005515	molecular_function	protein binding
m	0005737	cellular_component	cytoplasm
m	0005829	cellular_component	cytosol
m	0006508	biological_process	proteolysis
m	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
m	0008233	molecular_function	peptidase activity
m	0008236	molecular_function	serine-type peptidase activity
m	0009266	biological_process	response to temperature stimulus
m	0009314	biological_process	response to radiation
m	0009368	cellular_component	endopeptidase Clp complex
m	0009376	cellular_component	HslUV protease complex
m	0009408	biological_process	response to heat
m	0010498	biological_process	proteasomal protein catabolic process
m	0016020	cellular_component	membrane
m	0016787	molecular_function	hydrolase activity
m	0042802	molecular_function	identical protein binding
m	0043068	biological_process	positive regulation of programmed cell death
m	0051117	molecular_function	ATPase binding
n	0004176	molecular_function	ATP-dependent peptidase activity
n	0004252	molecular_function	serine-type endopeptidase activity
n	0005515	molecular_function	protein binding
n	0005737	cellular_component	cytoplasm
n	0005829	cellular_component	cytosol
n	0006508	biological_process	proteolysis
n	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
n	0008233	molecular_function	peptidase activity
n	0008236	molecular_function	serine-type peptidase activity
n	0009266	biological_process	response to temperature stimulus
n	0009314	biological_process	response to radiation
n	0009368	cellular_component	endopeptidase Clp complex
n	0009376	cellular_component	HslUV protease complex
n	0009408	biological_process	response to heat
n	0010498	biological_process	proteasomal protein catabolic process
n	0016020	cellular_component	membrane
n	0016787	molecular_function	hydrolase activity
n	0042802	molecular_function	identical protein binding
n	0043068	biological_process	positive regulation of programmed cell death
n	0051117	molecular_function	ATPase binding

Functional Information from PROSITE/UniProt

site_id	PS00381
Number of Residues	12
Details	CLP_PROTEASE_SER Endopeptidase Clp serine active site. TicMGqAASMGA

Chain	Residue	Details
H	THR89-ALA100

---

site_id	PS00382
Number of Residues	14
Details	CLP_PROTEASE_HIS Endopeptidase Clp histidine active site. RfclPnsrVMIHQP

Chain	Residue	Details
H	ARG111-PRO124

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	42
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00175","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19914167","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23622246","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	14
Details	Active site: {"description":"Nucleophile","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	28
Details	Active site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA10
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA11
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA12
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA13
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA14
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA2
Number of Residues	5
Details	M-CSA 912

Chain	Residue	Details
H	GLY68	electrostatic stabiliser
H	SER97	covalent catalysis, proton shuttle (general acid/base)
H	MET98	electrostatic stabiliser
H	HIS122	proton shuttle (general acid/base)
H	ASP171	electrostatic stabiliser, modifies pKa

---

site_id	MCSA3
Number of Residues	5
Details	M-CSA 912

Chain	Residue	Details
I	GLY68	electrostatic stabiliser
I	SER97	covalent catalysis, proton shuttle (general acid/base)
I	MET98	electrostatic stabiliser
I	HIS122	proton shuttle (general acid/base)
I	ASP171	electrostatic stabiliser, modifies pKa

---

site_id	MCSA4
Number of Residues	5
Details	M-CSA 912

Chain	Residue	Details
J	GLY68	electrostatic stabiliser
J	SER97	covalent catalysis, proton shuttle (general acid/base)
J	MET98	electrostatic stabiliser
J	HIS122	proton shuttle (general acid/base)
J	ASP171	electrostatic stabiliser, modifies pKa

---

site_id	MCSA5
Number of Residues	5
Details	M-CSA 912

Chain	Residue	Details
K	GLY68	electrostatic stabiliser
K	SER97	covalent catalysis, proton shuttle (general acid/base)
K	MET98	electrostatic stabiliser
K	HIS122	proton shuttle (general acid/base)
K	ASP171	electrostatic stabiliser, modifies pKa

---

site_id	MCSA6
Number of Residues	5
Details	M-CSA 912

Chain	Residue	Details
L	GLY68	electrostatic stabiliser
L	SER97	covalent catalysis, proton shuttle (general acid/base)
L	MET98	electrostatic stabiliser
L	HIS122	proton shuttle (general acid/base)
L	ASP171	electrostatic stabiliser, modifies pKa

---

site_id	MCSA7
Number of Residues	5
Details	M-CSA 912

Chain	Residue	Details
M	GLY68	electrostatic stabiliser
M	SER97	covalent catalysis, proton shuttle (general acid/base)
M	MET98	electrostatic stabiliser
M	HIS122	proton shuttle (general acid/base)
M	ASP171	electrostatic stabiliser, modifies pKa

---

site_id	MCSA8
Number of Residues	5
Details	M-CSA 912

Chain	Residue	Details
N	GLY68	electrostatic stabiliser
N	SER97	covalent catalysis, proton shuttle (general acid/base)
N	MET98	electrostatic stabiliser
N	HIS122	proton shuttle (general acid/base)
N	ASP171	electrostatic stabiliser, modifies pKa

---

site_id	MCSA9
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---