3DBR

Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006915	biological_process	apoptotic process
A	0007165	biological_process	signal transduction
A	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
A	0019781	molecular_function	NEDD8 activating enzyme activity
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0032991	cellular_component	protein-containing complex
A	0033314	biological_process	mitotic DNA replication checkpoint signaling
A	0042981	biological_process	regulation of apoptotic process
A	0043523	biological_process	regulation of neuron apoptotic process
A	0045116	biological_process	protein neddylation
A	0046982	molecular_function	protein heterodimerization activity
A	0051402	biological_process	neuron apoptotic process
A	0098978	cellular_component	glutamatergic synapse
A	0150052	biological_process	regulation of postsynapse assembly
B	0000166	molecular_function	nucleotide binding
B	0000278	biological_process	mitotic cell cycle
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006508	biological_process	proteolysis
B	0007113	biological_process	endomitotic cell cycle
B	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
B	0016874	molecular_function	ligase activity
B	0019781	molecular_function	NEDD8 activating enzyme activity
B	0019788	molecular_function	NEDD8 transferase activity
B	0032991	cellular_component	protein-containing complex
B	0036211	biological_process	protein modification process
B	0042802	molecular_function	identical protein binding
B	0043687	biological_process	post-translational protein modification
B	0045116	biological_process	protein neddylation
B	0046982	molecular_function	protein heterodimerization activity
B	0051726	biological_process	regulation of cell cycle
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0006915	biological_process	apoptotic process
C	0007165	biological_process	signal transduction
C	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
C	0019781	molecular_function	NEDD8 activating enzyme activity
C	0031625	molecular_function	ubiquitin protein ligase binding
C	0032991	cellular_component	protein-containing complex
C	0033314	biological_process	mitotic DNA replication checkpoint signaling
C	0042981	biological_process	regulation of apoptotic process
C	0043523	biological_process	regulation of neuron apoptotic process
C	0045116	biological_process	protein neddylation
C	0046982	molecular_function	protein heterodimerization activity
C	0051402	biological_process	neuron apoptotic process
C	0098978	cellular_component	glutamatergic synapse
C	0150052	biological_process	regulation of postsynapse assembly
D	0000166	molecular_function	nucleotide binding
D	0000278	biological_process	mitotic cell cycle
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006508	biological_process	proteolysis
D	0007113	biological_process	endomitotic cell cycle
D	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
D	0016874	molecular_function	ligase activity
D	0019781	molecular_function	NEDD8 activating enzyme activity
D	0019788	molecular_function	NEDD8 transferase activity
D	0032991	cellular_component	protein-containing complex
D	0036211	biological_process	protein modification process
D	0042802	molecular_function	identical protein binding
D	0043687	biological_process	post-translational protein modification
D	0045116	biological_process	protein neddylation
D	0046982	molecular_function	protein heterodimerization activity
D	0051726	biological_process	regulation of cell cycle
E	0005515	molecular_function	protein binding
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
E	0006915	biological_process	apoptotic process
E	0007165	biological_process	signal transduction
E	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
E	0019781	molecular_function	NEDD8 activating enzyme activity
E	0031625	molecular_function	ubiquitin protein ligase binding
E	0032991	cellular_component	protein-containing complex
E	0033314	biological_process	mitotic DNA replication checkpoint signaling
E	0042981	biological_process	regulation of apoptotic process
E	0043523	biological_process	regulation of neuron apoptotic process
E	0045116	biological_process	protein neddylation
E	0046982	molecular_function	protein heterodimerization activity
E	0051402	biological_process	neuron apoptotic process
E	0098978	cellular_component	glutamatergic synapse
E	0150052	biological_process	regulation of postsynapse assembly
F	0000166	molecular_function	nucleotide binding
F	0000278	biological_process	mitotic cell cycle
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006508	biological_process	proteolysis
F	0007113	biological_process	endomitotic cell cycle
F	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
F	0016874	molecular_function	ligase activity
F	0019781	molecular_function	NEDD8 activating enzyme activity
F	0019788	molecular_function	NEDD8 transferase activity
F	0032991	cellular_component	protein-containing complex
F	0036211	biological_process	protein modification process
F	0042802	molecular_function	identical protein binding
F	0043687	biological_process	post-translational protein modification
F	0045116	biological_process	protein neddylation
F	0046982	molecular_function	protein heterodimerization activity
F	0051726	biological_process	regulation of cell cycle
G	0005515	molecular_function	protein binding
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0005886	cellular_component	plasma membrane
G	0006915	biological_process	apoptotic process
G	0007165	biological_process	signal transduction
G	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
G	0019781	molecular_function	NEDD8 activating enzyme activity
G	0031625	molecular_function	ubiquitin protein ligase binding
G	0032991	cellular_component	protein-containing complex
G	0033314	biological_process	mitotic DNA replication checkpoint signaling
G	0042981	biological_process	regulation of apoptotic process
G	0043523	biological_process	regulation of neuron apoptotic process
G	0045116	biological_process	protein neddylation
G	0046982	molecular_function	protein heterodimerization activity
G	0051402	biological_process	neuron apoptotic process
G	0098978	cellular_component	glutamatergic synapse
G	0150052	biological_process	regulation of postsynapse assembly
H	0000166	molecular_function	nucleotide binding
H	0000278	biological_process	mitotic cell cycle
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005634	cellular_component	nucleus
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006508	biological_process	proteolysis
H	0007113	biological_process	endomitotic cell cycle
H	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
H	0016874	molecular_function	ligase activity
H	0019781	molecular_function	NEDD8 activating enzyme activity
H	0019788	molecular_function	NEDD8 transferase activity
H	0032991	cellular_component	protein-containing complex
H	0036211	biological_process	protein modification process
H	0042802	molecular_function	identical protein binding
H	0043687	biological_process	post-translational protein modification
H	0045116	biological_process	protein neddylation
H	0046982	molecular_function	protein heterodimerization activity
H	0051726	biological_process	regulation of cell cycle
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0006357	biological_process	regulation of transcription by RNA polymerase II
I	0006508	biological_process	proteolysis
I	0006511	biological_process	ubiquitin-dependent protein catabolic process
I	0008104	biological_process	intracellular protein localization
I	0009653	biological_process	anatomical structure morphogenesis
I	0016567	biological_process	protein ubiquitination
I	0019941	biological_process	modification-dependent protein catabolic process
I	0030162	biological_process	regulation of proteolysis
I	0031386	molecular_function	protein tag activity
I	0031625	molecular_function	ubiquitin protein ligase binding
I	0036211	biological_process	protein modification process
I	0045116	biological_process	protein neddylation
I	0070062	cellular_component	extracellular exosome
I	0072757	biological_process	cellular response to camptothecin
I	0098794	cellular_component	postsynapse
I	0098978	cellular_component	glutamatergic synapse
I	0150052	biological_process	regulation of postsynapse assembly
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0006357	biological_process	regulation of transcription by RNA polymerase II
J	0006508	biological_process	proteolysis
J	0006511	biological_process	ubiquitin-dependent protein catabolic process
J	0008104	biological_process	intracellular protein localization
J	0009653	biological_process	anatomical structure morphogenesis
J	0016567	biological_process	protein ubiquitination
J	0019941	biological_process	modification-dependent protein catabolic process
J	0030162	biological_process	regulation of proteolysis
J	0031386	molecular_function	protein tag activity
J	0031625	molecular_function	ubiquitin protein ligase binding
J	0036211	biological_process	protein modification process
J	0045116	biological_process	protein neddylation
J	0070062	cellular_component	extracellular exosome
J	0072757	biological_process	cellular response to camptothecin
J	0098794	cellular_component	postsynapse
J	0098978	cellular_component	glutamatergic synapse
J	0150052	biological_process	regulation of postsynapse assembly
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0006357	biological_process	regulation of transcription by RNA polymerase II
K	0006508	biological_process	proteolysis
K	0006511	biological_process	ubiquitin-dependent protein catabolic process
K	0008104	biological_process	intracellular protein localization
K	0009653	biological_process	anatomical structure morphogenesis
K	0016567	biological_process	protein ubiquitination
K	0019941	biological_process	modification-dependent protein catabolic process
K	0030162	biological_process	regulation of proteolysis
K	0031386	molecular_function	protein tag activity
K	0031625	molecular_function	ubiquitin protein ligase binding
K	0036211	biological_process	protein modification process
K	0045116	biological_process	protein neddylation
K	0070062	cellular_component	extracellular exosome
K	0072757	biological_process	cellular response to camptothecin
K	0098794	cellular_component	postsynapse
K	0098978	cellular_component	glutamatergic synapse
K	0150052	biological_process	regulation of postsynapse assembly
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0006357	biological_process	regulation of transcription by RNA polymerase II
L	0006508	biological_process	proteolysis
L	0006511	biological_process	ubiquitin-dependent protein catabolic process
L	0008104	biological_process	intracellular protein localization
L	0009653	biological_process	anatomical structure morphogenesis
L	0016567	biological_process	protein ubiquitination
L	0019941	biological_process	modification-dependent protein catabolic process
L	0030162	biological_process	regulation of proteolysis
L	0031386	molecular_function	protein tag activity
L	0031625	molecular_function	ubiquitin protein ligase binding
L	0036211	biological_process	protein modification process
L	0045116	biological_process	protein neddylation
L	0070062	cellular_component	extracellular exosome
L	0072757	biological_process	cellular response to camptothecin
L	0098794	cellular_component	postsynapse
L	0098978	cellular_component	glutamatergic synapse
L	0150052	biological_process	regulation of postsynapse assembly

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 1

Chain	Residue
B	CYS199
B	CYS202
B	CYS343
B	CYS346

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN H 2

Chain	Residue
H	CYS199
H	CYS202
H	CYS343
H	CYS346

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 3

Chain	Residue
D	CYS202
D	CYS343
D	CYS346
D	CYS199

---

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN F 4

Chain	Residue
F	CYS199
F	CYS202
F	CYS343
F	CYS346

---

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KerVeEkegIPpqqQrLIYsGkqmnD

Chain	Residue	Details
I	LYS127-ASP152

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	52
Details	Region: {"description":"Interaction with UBA3"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	3
Details	Site: {"description":"Interaction with UBA3"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q8VBW6","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	212
Details	Region: {"description":"Interaction with UBE2M N-terminus"}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	28
Details	Region: {"description":"Interaction with NEDD8"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	36
Details	Region: {"description":"Interaction with NAE1","evidences":[{"source":"PubMed","id":"12740388","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	95
Details	Region: {"description":"Interaction with UBE2M core domain"}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Active site: {"description":"Glycyl thioester intermediate"}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	188
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	Site: {"description":"Determines specificity for NEDD8"}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	8
Details	Region: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	8
Details	Site: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	Modified residue: {"description":"(Microbial infection) Deamidated glutamine","evidences":[{"source":"PubMed","id":"20688984","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21903097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23175788","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23589306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26632597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	8
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PubMed","id":"38316879","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---