9C87

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

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
p	0004176	molecular_function	ATP-dependent peptidase activity
p	0004252	molecular_function	serine-type endopeptidase activity
p	0005515	molecular_function	protein binding
p	0005737	cellular_component	cytoplasm
p	0005829	cellular_component	cytosol
p	0006508	biological_process	proteolysis
p	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
p	0008233	molecular_function	peptidase activity
p	0008236	molecular_function	serine-type peptidase activity
p	0009266	biological_process	response to temperature stimulus
p	0009314	biological_process	response to radiation
p	0009368	cellular_component	endopeptidase Clp complex
p	0009376	cellular_component	HslUV protease complex
p	0009408	biological_process	response to heat
p	0010498	biological_process	proteasomal protein catabolic process
p	0016020	cellular_component	membrane
p	0016787	molecular_function	hydrolase activity
p	0042802	molecular_function	identical protein binding
p	0043068	biological_process	positive regulation of programmed cell death
p	0051117	molecular_function	ATPase binding
q	0004176	molecular_function	ATP-dependent peptidase activity
q	0004252	molecular_function	serine-type endopeptidase activity
q	0005515	molecular_function	protein binding
q	0005737	cellular_component	cytoplasm
q	0005829	cellular_component	cytosol
q	0006508	biological_process	proteolysis
q	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
q	0008233	molecular_function	peptidase activity
q	0008236	molecular_function	serine-type peptidase activity
q	0009266	biological_process	response to temperature stimulus
q	0009314	biological_process	response to radiation
q	0009368	cellular_component	endopeptidase Clp complex
q	0009376	cellular_component	HslUV protease complex
q	0009408	biological_process	response to heat
q	0010498	biological_process	proteasomal protein catabolic process
q	0016020	cellular_component	membrane
q	0016787	molecular_function	hydrolase activity
q	0042802	molecular_function	identical protein binding
q	0043068	biological_process	positive regulation of programmed cell death
q	0051117	molecular_function	ATPase binding
r	0004176	molecular_function	ATP-dependent peptidase activity
r	0004252	molecular_function	serine-type endopeptidase activity
r	0005515	molecular_function	protein binding
r	0005737	cellular_component	cytoplasm
r	0005829	cellular_component	cytosol
r	0006508	biological_process	proteolysis
r	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
r	0008233	molecular_function	peptidase activity
r	0008236	molecular_function	serine-type peptidase activity
r	0009266	biological_process	response to temperature stimulus
r	0009314	biological_process	response to radiation
r	0009368	cellular_component	endopeptidase Clp complex
r	0009376	cellular_component	HslUV protease complex
r	0009408	biological_process	response to heat
r	0010498	biological_process	proteasomal protein catabolic process
r	0016020	cellular_component	membrane
r	0016787	molecular_function	hydrolase activity
r	0042802	molecular_function	identical protein binding
r	0043068	biological_process	positive regulation of programmed cell death
r	0051117	molecular_function	ATPase binding
s	0004176	molecular_function	ATP-dependent peptidase activity
s	0004252	molecular_function	serine-type endopeptidase activity
s	0005515	molecular_function	protein binding
s	0005737	cellular_component	cytoplasm
s	0005829	cellular_component	cytosol
s	0006508	biological_process	proteolysis
s	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
s	0008233	molecular_function	peptidase activity
s	0008236	molecular_function	serine-type peptidase activity
s	0009266	biological_process	response to temperature stimulus
s	0009314	biological_process	response to radiation
s	0009368	cellular_component	endopeptidase Clp complex
s	0009376	cellular_component	HslUV protease complex
s	0009408	biological_process	response to heat
s	0010498	biological_process	proteasomal protein catabolic process
s	0016020	cellular_component	membrane
s	0016787	molecular_function	hydrolase activity
s	0042802	molecular_function	identical protein binding
s	0043068	biological_process	positive regulation of programmed cell death
s	0051117	molecular_function	ATPase binding
S	0004146	molecular_function	dihydrofolate reductase activity
S	0005515	molecular_function	protein binding
S	0005542	molecular_function	folic acid binding
S	0005829	cellular_component	cytosol
S	0006730	biological_process	one-carbon metabolic process
S	0009257	biological_process	10-formyltetrahydrofolate biosynthetic process
S	0009410	biological_process	response to xenobiotic stimulus
S	0016491	molecular_function	oxidoreductase activity
S	0031427	biological_process	response to methotrexate
S	0044281	biological_process	small molecule metabolic process
S	0046452	biological_process	dihydrofolate metabolic process
S	0046654	biological_process	tetrahydrofolate biosynthetic process
S	0046655	biological_process	folic acid metabolic process
S	0046656	biological_process	folic acid biosynthetic process
S	0046677	biological_process	response to antibiotic
S	0050661	molecular_function	NADP binding
S	0051870	molecular_function	methotrexate binding
S	0051871	molecular_function	dihydrofolic acid binding
S	0070401	molecular_function	NADP+ binding
S	0070402	molecular_function	NADPH binding
t	0004176	molecular_function	ATP-dependent peptidase activity
t	0004252	molecular_function	serine-type endopeptidase activity
t	0005515	molecular_function	protein binding
t	0005737	cellular_component	cytoplasm
t	0005829	cellular_component	cytosol
t	0006508	biological_process	proteolysis
t	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
t	0008233	molecular_function	peptidase activity
t	0008236	molecular_function	serine-type peptidase activity
t	0009266	biological_process	response to temperature stimulus
t	0009314	biological_process	response to radiation
t	0009368	cellular_component	endopeptidase Clp complex
t	0009376	cellular_component	HslUV protease complex
t	0009408	biological_process	response to heat
t	0010498	biological_process	proteasomal protein catabolic process
t	0016020	cellular_component	membrane
t	0016787	molecular_function	hydrolase activity
t	0042802	molecular_function	identical protein binding
t	0043068	biological_process	positive regulation of programmed cell death
t	0051117	molecular_function	ATPase binding
u	0004176	molecular_function	ATP-dependent peptidase activity
u	0004252	molecular_function	serine-type endopeptidase activity
u	0005515	molecular_function	protein binding
u	0005737	cellular_component	cytoplasm
u	0005829	cellular_component	cytosol
u	0006508	biological_process	proteolysis
u	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
u	0008233	molecular_function	peptidase activity
u	0008236	molecular_function	serine-type peptidase activity
u	0009266	biological_process	response to temperature stimulus
u	0009314	biological_process	response to radiation
u	0009368	cellular_component	endopeptidase Clp complex
u	0009376	cellular_component	HslUV protease complex
u	0009408	biological_process	response to heat
u	0010498	biological_process	proteasomal protein catabolic process
u	0016020	cellular_component	membrane
u	0016787	molecular_function	hydrolase activity
u	0042802	molecular_function	identical protein binding
u	0043068	biological_process	positive regulation of programmed cell death
u	0051117	molecular_function	ATPase binding
v	0004176	molecular_function	ATP-dependent peptidase activity
v	0004252	molecular_function	serine-type endopeptidase activity
v	0005515	molecular_function	protein binding
v	0005737	cellular_component	cytoplasm
v	0005829	cellular_component	cytosol
v	0006508	biological_process	proteolysis
v	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
v	0008233	molecular_function	peptidase activity
v	0008236	molecular_function	serine-type peptidase activity
v	0009266	biological_process	response to temperature stimulus
v	0009314	biological_process	response to radiation
v	0009368	cellular_component	endopeptidase Clp complex
v	0009376	cellular_component	HslUV protease complex
v	0009408	biological_process	response to heat
v	0010498	biological_process	proteasomal protein catabolic process
v	0016020	cellular_component	membrane
v	0016787	molecular_function	hydrolase activity
v	0042802	molecular_function	identical protein binding
v	0043068	biological_process	positive regulation of programmed cell death
v	0051117	molecular_function	ATPase binding

Functional Information from PROSITE/UniProt

site_id	PS00075
Number of Residues	23
Details	DHFR_1 Dihydrofolate reductase (DHFR) domain signature. VIGmenaMPWnlpa.DlawFkrnT

Chain	Residue	Details
S	VAL13-THR35

---

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	5
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9012674","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	17
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19374017","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	14
Details	Active site: {"description":"Nucleophile","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
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
S	LEU54	electrostatic stabiliser
S	ALA83	covalent catalysis, proton shuttle (general acid/base)
S	ALA84	electrostatic stabiliser
S	GLN108	proton shuttle (general acid/base)
S	GLU157	electrostatic stabiliser, modifies pKa

---

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

---

site_id	MCSA3
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA4
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA5
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA6
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA7
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA8
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---

site_id	MCSA9
Number of Residues	5
Details	M-CSA 912

Chain

Residue

Details

---