6S53

Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004842	molecular_function	ubiquitin-protein transferase activity
A	0016567	biological_process	protein ubiquitination
A	0046872	molecular_function	metal ion binding
B	0004842	molecular_function	ubiquitin-protein transferase activity
B	0016567	biological_process	protein ubiquitination
B	0046872	molecular_function	metal ion binding
C	0000151	cellular_component	ubiquitin ligase complex
C	0000166	molecular_function	nucleotide binding
C	0000209	biological_process	protein polyubiquitination
C	0000724	biological_process	double-strand break repair via homologous recombination
C	0000729	biological_process	DNA double-strand break processing
C	0003723	molecular_function	RNA binding
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006281	biological_process	DNA repair
C	0006282	biological_process	regulation of DNA repair
C	0006301	biological_process	postreplication repair
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0006513	biological_process	protein monoubiquitination
C	0006974	biological_process	DNA damage response
C	0016567	biological_process	protein ubiquitination
C	0016740	molecular_function	transferase activity
C	0031371	cellular_component	ubiquitin conjugating enzyme complex
C	0031372	cellular_component	UBC13-MMS2 complex
C	0031625	molecular_function	ubiquitin protein ligase binding
C	0031669	biological_process	cellular response to nutrient levels
C	0032991	cellular_component	protein-containing complex
C	0038202	biological_process	TORC1 signaling
C	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
C	0043130	molecular_function	ubiquitin binding
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0045739	biological_process	positive regulation of DNA repair
C	0050852	biological_process	T cell receptor signaling pathway
C	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
C	0061631	molecular_function	ubiquitin conjugating enzyme activity
C	0070062	cellular_component	extracellular exosome
C	0070534	biological_process	protein K63-linked ubiquitination
C	0097027	molecular_function	ubiquitin-protein transferase activator activity
C	0140374	biological_process	antiviral innate immune response
C	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
C	1902533	biological_process	positive regulation of intracellular signal transduction
C	1904262	biological_process	negative regulation of TORC1 signaling
C	2000781	biological_process	positive regulation of double-strand break repair
E	0000151	cellular_component	ubiquitin ligase complex
E	0000166	molecular_function	nucleotide binding
E	0000209	biological_process	protein polyubiquitination
E	0000724	biological_process	double-strand break repair via homologous recombination
E	0000729	biological_process	DNA double-strand break processing
E	0003723	molecular_function	RNA binding
E	0004842	molecular_function	ubiquitin-protein transferase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006281	biological_process	DNA repair
E	0006282	biological_process	regulation of DNA repair
E	0006301	biological_process	postreplication repair
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0006513	biological_process	protein monoubiquitination
E	0006974	biological_process	DNA damage response
E	0016567	biological_process	protein ubiquitination
E	0016740	molecular_function	transferase activity
E	0031371	cellular_component	ubiquitin conjugating enzyme complex
E	0031372	cellular_component	UBC13-MMS2 complex
E	0031625	molecular_function	ubiquitin protein ligase binding
E	0031669	biological_process	cellular response to nutrient levels
E	0032991	cellular_component	protein-containing complex
E	0038202	biological_process	TORC1 signaling
E	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
E	0043130	molecular_function	ubiquitin binding
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0045739	biological_process	positive regulation of DNA repair
E	0050852	biological_process	T cell receptor signaling pathway
E	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
E	0061631	molecular_function	ubiquitin conjugating enzyme activity
E	0070062	cellular_component	extracellular exosome
E	0070534	biological_process	protein K63-linked ubiquitination
E	0097027	molecular_function	ubiquitin-protein transferase activator activity
E	0140374	biological_process	antiviral innate immune response
E	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
E	1902533	biological_process	positive regulation of intracellular signal transduction
E	1904262	biological_process	negative regulation of TORC1 signaling
E	2000781	biological_process	positive regulation of double-strand break repair
G	0004842	molecular_function	ubiquitin-protein transferase activity
G	0016567	biological_process	protein ubiquitination
G	0046872	molecular_function	metal ion binding
H	0004842	molecular_function	ubiquitin-protein transferase activity
H	0016567	biological_process	protein ubiquitination
H	0046872	molecular_function	metal ion binding
I	0000151	cellular_component	ubiquitin ligase complex
I	0000166	molecular_function	nucleotide binding
I	0000209	biological_process	protein polyubiquitination
I	0000724	biological_process	double-strand break repair via homologous recombination
I	0000729	biological_process	DNA double-strand break processing
I	0003723	molecular_function	RNA binding
I	0004842	molecular_function	ubiquitin-protein transferase activity
I	0005515	molecular_function	protein binding
I	0005524	molecular_function	ATP binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0006281	biological_process	DNA repair
I	0006282	biological_process	regulation of DNA repair
I	0006301	biological_process	postreplication repair
I	0006511	biological_process	ubiquitin-dependent protein catabolic process
I	0006513	biological_process	protein monoubiquitination
I	0006974	biological_process	DNA damage response
I	0016567	biological_process	protein ubiquitination
I	0016740	molecular_function	transferase activity
I	0031371	cellular_component	ubiquitin conjugating enzyme complex
I	0031372	cellular_component	UBC13-MMS2 complex
I	0031625	molecular_function	ubiquitin protein ligase binding
I	0031669	biological_process	cellular response to nutrient levels
I	0032991	cellular_component	protein-containing complex
I	0038202	biological_process	TORC1 signaling
I	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
I	0043130	molecular_function	ubiquitin binding
I	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
I	0045739	biological_process	positive regulation of DNA repair
I	0050852	biological_process	T cell receptor signaling pathway
I	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
I	0061631	molecular_function	ubiquitin conjugating enzyme activity
I	0070062	cellular_component	extracellular exosome
I	0070534	biological_process	protein K63-linked ubiquitination
I	0097027	molecular_function	ubiquitin-protein transferase activator activity
I	0140374	biological_process	antiviral innate immune response
I	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
I	1902533	biological_process	positive regulation of intracellular signal transduction
I	1904262	biological_process	negative regulation of TORC1 signaling
I	2000781	biological_process	positive regulation of double-strand break repair
K	0000151	cellular_component	ubiquitin ligase complex
K	0000166	molecular_function	nucleotide binding
K	0000209	biological_process	protein polyubiquitination
K	0000724	biological_process	double-strand break repair via homologous recombination
K	0000729	biological_process	DNA double-strand break processing
K	0003723	molecular_function	RNA binding
K	0004842	molecular_function	ubiquitin-protein transferase activity
K	0005515	molecular_function	protein binding
K	0005524	molecular_function	ATP binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0006281	biological_process	DNA repair
K	0006282	biological_process	regulation of DNA repair
K	0006301	biological_process	postreplication repair
K	0006511	biological_process	ubiquitin-dependent protein catabolic process
K	0006513	biological_process	protein monoubiquitination
K	0006974	biological_process	DNA damage response
K	0016567	biological_process	protein ubiquitination
K	0016740	molecular_function	transferase activity
K	0031371	cellular_component	ubiquitin conjugating enzyme complex
K	0031372	cellular_component	UBC13-MMS2 complex
K	0031625	molecular_function	ubiquitin protein ligase binding
K	0031669	biological_process	cellular response to nutrient levels
K	0032991	cellular_component	protein-containing complex
K	0038202	biological_process	TORC1 signaling
K	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
K	0043130	molecular_function	ubiquitin binding
K	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
K	0045739	biological_process	positive regulation of DNA repair
K	0050852	biological_process	T cell receptor signaling pathway
K	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
K	0061631	molecular_function	ubiquitin conjugating enzyme activity
K	0070062	cellular_component	extracellular exosome
K	0070534	biological_process	protein K63-linked ubiquitination
K	0097027	molecular_function	ubiquitin-protein transferase activator activity
K	0140374	biological_process	antiviral innate immune response
K	1902523	biological_process	positive regulation of protein K63-linked ubiquitination
K	1902533	biological_process	positive regulation of intracellular signal transduction
K	1904262	biological_process	negative regulation of TORC1 signaling
K	2000781	biological_process	positive regulation of double-strand break repair

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN B 101

Chain	Residue
B	CYS16
B	CYS19
B	CYS36
B	CYS39

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN B 102

Chain	Residue
B	CYS31
B	HIS33
B	CYS51
B	CYS54

---

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN A 101

Chain	Residue
A	CYS19
A	CYS36
A	CYS39
A	CYS16

---

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN A 102

Chain	Residue
A	CYS31
A	HIS33
A	CYS51
A	CYS54

---

site_id	AC5
Number of Residues	5
Details	binding site for residue MPD A 103

Chain	Residue
A	GLU30
A	ASN62
A	ARG64
B	ASN62
B	ARG64

---

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN H 101

Chain	Residue
H	CYS31
H	HIS33
H	CYS51
H	CYS54

---

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN H 102

Chain	Residue
H	CYS16
H	CYS19
H	CYS36
H	CYS39

---

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN G 101

Chain	Residue
G	CYS31
G	HIS33
G	CYS51
G	CYS54

---

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN G 102

Chain	Residue
G	CYS16
G	CYS19
G	CYS36
G	CYS39

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
F	LYS27-ASP52

---

site_id	PS00518
Number of Residues	10
Details	ZF_RING_1 Zinc finger RING-type signature. CgHsFCqeCI

Chain	Residue	Details
B	CYS31-ILE40

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
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_FI3
Number of Residues	8
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15)","evidences":[{"source":"PubMed","id":"16112642","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16122702","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	300
Details	Domain: {"description":"Ubiquitin-like 9","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	117
Details	Zinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---