3E47

Crystal Structure of the Yeast 20S Proteasome in Complex with Homobelactosin C

Replaces:  2FNY

Functional Information from GO Data

Chain	GOid	namespace	contents
1	0005839	cellular_component	proteasome core complex
1	0051603	biological_process	proteolysis involved in protein catabolic process
2	0000502	cellular_component	proteasome complex
2	0004175	molecular_function	endopeptidase activity
2	0004298	molecular_function	threonine-type endopeptidase activity
2	0005515	molecular_function	protein binding
2	0005634	cellular_component	nucleus
2	0005737	cellular_component	cytoplasm
2	0005829	cellular_component	cytosol
2	0005839	cellular_component	proteasome core complex
2	0006508	biological_process	proteolysis
2	0008233	molecular_function	peptidase activity
2	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
2	0016787	molecular_function	hydrolase activity
2	0019774	cellular_component	proteasome core complex, beta-subunit complex
2	0034515	cellular_component	proteasome storage granule
2	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
2	0051603	biological_process	proteolysis involved in protein catabolic process
A	0000502	cellular_component	proteasome complex
A	0003674	molecular_function	molecular_function
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005839	cellular_component	proteasome core complex
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
A	0019773	cellular_component	proteasome core complex, alpha-subunit complex
A	0034515	cellular_component	proteasome storage granule
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0051603	biological_process	proteolysis involved in protein catabolic process
B	0000502	cellular_component	proteasome complex
B	0003674	molecular_function	molecular_function
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005839	cellular_component	proteasome core complex
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
B	0019773	cellular_component	proteasome core complex, alpha-subunit complex
B	0034515	cellular_component	proteasome storage granule
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0051603	biological_process	proteolysis involved in protein catabolic process
B	0080129	biological_process	proteasome core complex assembly
C	0000502	cellular_component	proteasome complex
C	0003674	molecular_function	molecular_function
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005839	cellular_component	proteasome core complex
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
C	0019773	cellular_component	proteasome core complex, alpha-subunit complex
C	0034515	cellular_component	proteasome storage granule
C	0042175	cellular_component	nuclear outer membrane-endoplasmic reticulum membrane network
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0051603	biological_process	proteolysis involved in protein catabolic process
D	0000502	cellular_component	proteasome complex
D	0003674	molecular_function	molecular_function
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005839	cellular_component	proteasome core complex
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
D	0019773	cellular_component	proteasome core complex, alpha-subunit complex
D	0034515	cellular_component	proteasome storage granule
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0051603	biological_process	proteolysis involved in protein catabolic process
E	0000502	cellular_component	proteasome complex
E	0003674	molecular_function	molecular_function
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005839	cellular_component	proteasome core complex
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
E	0019773	cellular_component	proteasome core complex, alpha-subunit complex
E	0034515	cellular_component	proteasome storage granule
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0051603	biological_process	proteolysis involved in protein catabolic process
F	0005839	cellular_component	proteasome core complex
F	0006511	biological_process	ubiquitin-dependent protein catabolic process
F	0019773	cellular_component	proteasome core complex, alpha-subunit complex
F	0051603	biological_process	proteolysis involved in protein catabolic process
G	0000502	cellular_component	proteasome complex
G	0003674	molecular_function	molecular_function
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0005739	cellular_component	mitochondrion
G	0005829	cellular_component	cytosol
G	0005839	cellular_component	proteasome core complex
G	0006511	biological_process	ubiquitin-dependent protein catabolic process
G	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
G	0019773	cellular_component	proteasome core complex, alpha-subunit complex
G	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
G	0051603	biological_process	proteolysis involved in protein catabolic process
H	0004298	molecular_function	threonine-type endopeptidase activity
H	0005839	cellular_component	proteasome core complex
H	0051603	biological_process	proteolysis involved in protein catabolic process
I	0000502	cellular_component	proteasome complex
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0005839	cellular_component	proteasome core complex
I	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
I	0019774	cellular_component	proteasome core complex, beta-subunit complex
I	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
I	0051603	biological_process	proteolysis involved in protein catabolic process
I	0061133	molecular_function	endopeptidase activator activity
J	0000502	cellular_component	proteasome complex
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005737	cellular_component	cytoplasm
J	0005789	cellular_component	endoplasmic reticulum membrane
J	0005829	cellular_component	cytosol
J	0005839	cellular_component	proteasome core complex
J	0010498	biological_process	proteasomal protein catabolic process
J	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
J	0019774	cellular_component	proteasome core complex, beta-subunit complex
J	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
J	0051603	biological_process	proteolysis involved in protein catabolic process
J	0061133	molecular_function	endopeptidase activator activity
K	0004298	molecular_function	threonine-type endopeptidase activity
K	0005839	cellular_component	proteasome core complex
K	0051603	biological_process	proteolysis involved in protein catabolic process
L	0000502	cellular_component	proteasome complex
L	0003674	molecular_function	molecular_function
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0005839	cellular_component	proteasome core complex
L	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
L	0019774	cellular_component	proteasome core complex, beta-subunit complex
L	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
L	0051603	biological_process	proteolysis involved in protein catabolic process
M	0005839	cellular_component	proteasome core complex
M	0051603	biological_process	proteolysis involved in protein catabolic process
N	0000502	cellular_component	proteasome complex
N	0004175	molecular_function	endopeptidase activity
N	0004298	molecular_function	threonine-type endopeptidase activity
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005737	cellular_component	cytoplasm
N	0005829	cellular_component	cytosol
N	0005839	cellular_component	proteasome core complex
N	0006508	biological_process	proteolysis
N	0008233	molecular_function	peptidase activity
N	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
N	0016787	molecular_function	hydrolase activity
N	0019774	cellular_component	proteasome core complex, beta-subunit complex
N	0034515	cellular_component	proteasome storage granule
N	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
N	0051603	biological_process	proteolysis involved in protein catabolic process
O	0000502	cellular_component	proteasome complex
O	0003674	molecular_function	molecular_function
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005737	cellular_component	cytoplasm
O	0005839	cellular_component	proteasome core complex
O	0006511	biological_process	ubiquitin-dependent protein catabolic process
O	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
O	0019773	cellular_component	proteasome core complex, alpha-subunit complex
O	0034515	cellular_component	proteasome storage granule
O	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
O	0051603	biological_process	proteolysis involved in protein catabolic process
P	0000502	cellular_component	proteasome complex
P	0003674	molecular_function	molecular_function
P	0005515	molecular_function	protein binding
P	0005634	cellular_component	nucleus
P	0005737	cellular_component	cytoplasm
P	0005829	cellular_component	cytosol
P	0005839	cellular_component	proteasome core complex
P	0006511	biological_process	ubiquitin-dependent protein catabolic process
P	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
P	0019773	cellular_component	proteasome core complex, alpha-subunit complex
P	0034515	cellular_component	proteasome storage granule
P	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
P	0051603	biological_process	proteolysis involved in protein catabolic process
P	0080129	biological_process	proteasome core complex assembly
Q	0000502	cellular_component	proteasome complex
Q	0003674	molecular_function	molecular_function
Q	0005515	molecular_function	protein binding
Q	0005634	cellular_component	nucleus
Q	0005737	cellular_component	cytoplasm
Q	0005739	cellular_component	mitochondrion
Q	0005839	cellular_component	proteasome core complex
Q	0006511	biological_process	ubiquitin-dependent protein catabolic process
Q	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
Q	0019773	cellular_component	proteasome core complex, alpha-subunit complex
Q	0034515	cellular_component	proteasome storage granule
Q	0042175	cellular_component	nuclear outer membrane-endoplasmic reticulum membrane network
Q	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
Q	0051603	biological_process	proteolysis involved in protein catabolic process
R	0000502	cellular_component	proteasome complex
R	0003674	molecular_function	molecular_function
R	0005515	molecular_function	protein binding
R	0005634	cellular_component	nucleus
R	0005737	cellular_component	cytoplasm
R	0005839	cellular_component	proteasome core complex
R	0006511	biological_process	ubiquitin-dependent protein catabolic process
R	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
R	0019773	cellular_component	proteasome core complex, alpha-subunit complex
R	0034515	cellular_component	proteasome storage granule
R	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
R	0051603	biological_process	proteolysis involved in protein catabolic process
S	0000502	cellular_component	proteasome complex
S	0003674	molecular_function	molecular_function
S	0005515	molecular_function	protein binding
S	0005634	cellular_component	nucleus
S	0005737	cellular_component	cytoplasm
S	0005839	cellular_component	proteasome core complex
S	0006511	biological_process	ubiquitin-dependent protein catabolic process
S	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
S	0019773	cellular_component	proteasome core complex, alpha-subunit complex
S	0034515	cellular_component	proteasome storage granule
S	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
S	0051603	biological_process	proteolysis involved in protein catabolic process
T	0005839	cellular_component	proteasome core complex
T	0006511	biological_process	ubiquitin-dependent protein catabolic process
T	0019773	cellular_component	proteasome core complex, alpha-subunit complex
T	0051603	biological_process	proteolysis involved in protein catabolic process
U	0000502	cellular_component	proteasome complex
U	0003674	molecular_function	molecular_function
U	0005515	molecular_function	protein binding
U	0005634	cellular_component	nucleus
U	0005737	cellular_component	cytoplasm
U	0005739	cellular_component	mitochondrion
U	0005829	cellular_component	cytosol
U	0005839	cellular_component	proteasome core complex
U	0006511	biological_process	ubiquitin-dependent protein catabolic process
U	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
U	0019773	cellular_component	proteasome core complex, alpha-subunit complex
U	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
U	0051603	biological_process	proteolysis involved in protein catabolic process
V	0004298	molecular_function	threonine-type endopeptidase activity
V	0005839	cellular_component	proteasome core complex
V	0051603	biological_process	proteolysis involved in protein catabolic process
W	0000502	cellular_component	proteasome complex
W	0005515	molecular_function	protein binding
W	0005634	cellular_component	nucleus
W	0005737	cellular_component	cytoplasm
W	0005829	cellular_component	cytosol
W	0005839	cellular_component	proteasome core complex
W	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
W	0019774	cellular_component	proteasome core complex, beta-subunit complex
W	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
W	0051603	biological_process	proteolysis involved in protein catabolic process
W	0061133	molecular_function	endopeptidase activator activity
X	0000502	cellular_component	proteasome complex
X	0005515	molecular_function	protein binding
X	0005634	cellular_component	nucleus
X	0005737	cellular_component	cytoplasm
X	0005789	cellular_component	endoplasmic reticulum membrane
X	0005829	cellular_component	cytosol
X	0005839	cellular_component	proteasome core complex
X	0010498	biological_process	proteasomal protein catabolic process
X	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
X	0019774	cellular_component	proteasome core complex, beta-subunit complex
X	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
X	0051603	biological_process	proteolysis involved in protein catabolic process
X	0061133	molecular_function	endopeptidase activator activity
Y	0004298	molecular_function	threonine-type endopeptidase activity
Y	0005839	cellular_component	proteasome core complex
Y	0051603	biological_process	proteolysis involved in protein catabolic process
Z	0000502	cellular_component	proteasome complex
Z	0003674	molecular_function	molecular_function
Z	0005515	molecular_function	protein binding
Z	0005634	cellular_component	nucleus
Z	0005737	cellular_component	cytoplasm
Z	0005829	cellular_component	cytosol
Z	0005839	cellular_component	proteasome core complex
Z	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
Z	0019774	cellular_component	proteasome core complex, beta-subunit complex
Z	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
Z	0051603	biological_process	proteolysis involved in protein catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ESY K 2000

Chain	Residue
J	ILE24
K	SER115
K	GLY128
K	SER129
K	GLN131
W	SER24
X	PHE132
K	THR1
K	ARG19
K	LYS33
K	MET45
K	ALA46
K	GLY47
K	GLY98
K	TYR112

---

site_id	AC2
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ESY Y 2000

Chain	Residue
I	SER24
J	PHE132
X	ILE24
Y	THR1
Y	ARG19
Y	LYS33
Y	MET45
Y	ALA46
Y	GLY47
Y	GLY98
Y	TYR112
Y	SER115
Y	GLY128
Y	SER129
Y	GLN131

---

Functional Information from PROSITE/UniProt

site_id	PS00388
Number of Residues	23
Details	PROTEASOME_ALPHA_1 Proteasome alpha-type subunits signature. YdrhiTiFSPeGRlyQVEYAfkA

Chain	Residue	Details
G	TYR8-ALA30
C	TYR8-ALA30
E	TYR8-ALA30
F	TYR8-ALA30
B	TYR8-SER30
A	TYR8-ALA30

---

site_id	PS00854
Number of Residues	48
Details	PROTEASOME_BETA_1 Proteasome beta-type subunits signature. LGIaGedFAVLAGDtrnitdysinsryep.KvfdcgdnivmsanGfaAD

Chain	Residue	Details
L	LEU4-ASP51
1	ILE4-ASP51
C	VAL38-ASP84
2	MET4-ASP51
J	LEU4-ASP51
K	LEU4-ASP51
I	VAL4-ASP51
B	ILE38-ASP84
H	VAL4-ASP51

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	24
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	6
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	6
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"9087403","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Binding site: {}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	4
Details	Annotated By Reference To The Literature 1pma

Chain	Residue	Details
D	GLY80
D	SER35
D	SER167
D	LYS66

---

site_id	CSA2
Number of Residues	4
Details	Annotated By Reference To The Literature 1pma

Chain	Residue	Details
R	GLY80
R	SER35
R	SER167
R	LYS66

---

site_id	CSA3
Number of Residues	4
Details	Annotated By Reference To The Literature 1pma

Chain	Residue	Details
K	GLY47
K	LYS33
K	THR1
K	SER129

---

site_id	CSA4
Number of Residues	4
Details	Annotated By Reference To The Literature 1pma

Chain	Residue	Details
Y	GLY47
Y	LYS33
Y	THR1
Y	SER129

---

site_id	CSA5
Number of Residues	4
Details	Annotated By Reference To The Literature 1pma

Chain	Residue	Details
H	GLY47
H	LYS33
H	THR1
H	SER129

---

site_id	CSA6
Number of Residues	4
Details	Annotated By Reference To The Literature 1pma

Chain	Residue	Details
V	GLY47
V	LYS33
V	THR1
V	SER129

---

site_id	CSA7
Number of Residues	4
Details	Annotated By Reference To The Literature 1pma

Chain	Residue	Details
N	GLY47
N	LYS33
N	THR1
N	SER129

---

site_id	CSA8
Number of Residues	4
Details	Annotated By Reference To The Literature 1pma

Chain	Residue	Details
2	GLY47
2	LYS33
2	THR1
2	SER129

---

site_id	MCSA1
Number of Residues	8
Details	M-CSA 177

Chain	Residue	Details
H	THR1	covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
H	ASP17	activator, steric locator
H	ARG19	activator
H	LYS33	activator, electrostatic stabiliser
H	GLY47	electrostatic stabiliser
H	SER129	activator, electrostatic stabiliser
H	ASP166	activator, steric locator
H	SER169	activator, electrostatic stabiliser

---

site_id	MCSA2
Number of Residues	8
Details	M-CSA 177

Chain	Residue	Details
V	THR1	covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
V	ASP17	activator, steric locator
V	ARG19	activator
V	LYS33	activator, electrostatic stabiliser
V	GLY47	electrostatic stabiliser
V	SER129	activator, electrostatic stabiliser
V	ASP166	activator, steric locator
V	SER169	activator, electrostatic stabiliser

---