6ZHU

Yeast Uba1 in complex with Ubc3 and ATP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004839	molecular_function	ubiquitin activating enzyme activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0006974	biological_process	DNA damage response
A	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
A	0016567	biological_process	protein ubiquitination
A	0016874	molecular_function	ligase activity
A	0036211	biological_process	protein modification process
A	0046872	molecular_function	metal ion binding
B	0000082	biological_process	G1/S transition of mitotic cell cycle
B	0000086	biological_process	G2/M transition of mitotic cell cycle
B	0000166	molecular_function	nucleotide binding
B	0000209	biological_process	protein polyubiquitination
B	0000409	biological_process	regulation of transcription by galactose
B	0000781	cellular_component	chromosome, telomeric region
B	0004842	molecular_function	ubiquitin-protein transferase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0006260	biological_process	DNA replication
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0007346	biological_process	regulation of mitotic cell cycle
B	0008053	biological_process	mitochondrial fusion
B	0010828	biological_process	positive regulation of D-glucose transmembrane transport
B	0016567	biological_process	protein ubiquitination
B	0016740	molecular_function	transferase activity
B	0019005	cellular_component	SCF ubiquitin ligase complex
B	0030466	biological_process	silent mating-type cassette heterochromatin formation
B	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
B	0031509	biological_process	subtelomeric heterochromatin formation
B	0031573	biological_process	mitotic intra-S DNA damage checkpoint signaling
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0051301	biological_process	cell division
B	0051865	biological_process	protein autoubiquitination
B	0061630	molecular_function	ubiquitin protein ligase activity
B	0061631	molecular_function	ubiquitin conjugating enzyme activity
B	0071406	biological_process	cellular response to methylmercury
C	0000166	molecular_function	nucleotide binding
C	0004839	molecular_function	ubiquitin activating enzyme activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0006974	biological_process	DNA damage response
C	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
C	0016567	biological_process	protein ubiquitination
C	0016874	molecular_function	ligase activity
C	0036211	biological_process	protein modification process
C	0046872	molecular_function	metal ion binding
D	0000082	biological_process	G1/S transition of mitotic cell cycle
D	0000086	biological_process	G2/M transition of mitotic cell cycle
D	0000166	molecular_function	nucleotide binding
D	0000209	biological_process	protein polyubiquitination
D	0000409	biological_process	regulation of transcription by galactose
D	0000781	cellular_component	chromosome, telomeric region
D	0004842	molecular_function	ubiquitin-protein transferase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0006260	biological_process	DNA replication
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0007346	biological_process	regulation of mitotic cell cycle
D	0008053	biological_process	mitochondrial fusion
D	0010828	biological_process	positive regulation of D-glucose transmembrane transport
D	0016567	biological_process	protein ubiquitination
D	0016740	molecular_function	transferase activity
D	0019005	cellular_component	SCF ubiquitin ligase complex
D	0030466	biological_process	silent mating-type cassette heterochromatin formation
D	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
D	0031509	biological_process	subtelomeric heterochromatin formation
D	0031573	biological_process	mitotic intra-S DNA damage checkpoint signaling
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0051301	biological_process	cell division
D	0051865	biological_process	protein autoubiquitination
D	0061630	molecular_function	ubiquitin protein ligase activity
D	0061631	molecular_function	ubiquitin conjugating enzyme activity
D	0071406	biological_process	cellular response to methylmercury
E	0000166	molecular_function	nucleotide binding
E	0004839	molecular_function	ubiquitin activating enzyme activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0006974	biological_process	DNA damage response
E	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
E	0016567	biological_process	protein ubiquitination
E	0016874	molecular_function	ligase activity
E	0036211	biological_process	protein modification process
E	0046872	molecular_function	metal ion binding
F	0000082	biological_process	G1/S transition of mitotic cell cycle
F	0000086	biological_process	G2/M transition of mitotic cell cycle
F	0000166	molecular_function	nucleotide binding
F	0000209	biological_process	protein polyubiquitination
F	0000409	biological_process	regulation of transcription by galactose
F	0000781	cellular_component	chromosome, telomeric region
F	0004842	molecular_function	ubiquitin-protein transferase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0006260	biological_process	DNA replication
F	0006511	biological_process	ubiquitin-dependent protein catabolic process
F	0007346	biological_process	regulation of mitotic cell cycle
F	0008053	biological_process	mitochondrial fusion
F	0010828	biological_process	positive regulation of D-glucose transmembrane transport
F	0016567	biological_process	protein ubiquitination
F	0016740	molecular_function	transferase activity
F	0019005	cellular_component	SCF ubiquitin ligase complex
F	0030466	biological_process	silent mating-type cassette heterochromatin formation
F	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
F	0031509	biological_process	subtelomeric heterochromatin formation
F	0031573	biological_process	mitotic intra-S DNA damage checkpoint signaling
F	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
F	0051301	biological_process	cell division
F	0051865	biological_process	protein autoubiquitination
F	0061630	molecular_function	ubiquitin protein ligase activity
F	0061631	molecular_function	ubiquitin conjugating enzyme activity
F	0071406	biological_process	cellular response to methylmercury
G	0000166	molecular_function	nucleotide binding
G	0004839	molecular_function	ubiquitin activating enzyme activity
G	0005515	molecular_function	protein binding
G	0005524	molecular_function	ATP binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0006511	biological_process	ubiquitin-dependent protein catabolic process
G	0006974	biological_process	DNA damage response
G	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
G	0016567	biological_process	protein ubiquitination
G	0016874	molecular_function	ligase activity
G	0036211	biological_process	protein modification process
G	0046872	molecular_function	metal ion binding
H	0000082	biological_process	G1/S transition of mitotic cell cycle
H	0000086	biological_process	G2/M transition of mitotic cell cycle
H	0000166	molecular_function	nucleotide binding
H	0000209	biological_process	protein polyubiquitination
H	0000409	biological_process	regulation of transcription by galactose
H	0000781	cellular_component	chromosome, telomeric region
H	0004842	molecular_function	ubiquitin-protein transferase activity
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005634	cellular_component	nucleus
H	0005737	cellular_component	cytoplasm
H	0006260	biological_process	DNA replication
H	0006511	biological_process	ubiquitin-dependent protein catabolic process
H	0007346	biological_process	regulation of mitotic cell cycle
H	0008053	biological_process	mitochondrial fusion
H	0010828	biological_process	positive regulation of D-glucose transmembrane transport
H	0016567	biological_process	protein ubiquitination
H	0016740	molecular_function	transferase activity
H	0019005	cellular_component	SCF ubiquitin ligase complex
H	0030466	biological_process	silent mating-type cassette heterochromatin formation
H	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
H	0031509	biological_process	subtelomeric heterochromatin formation
H	0031573	biological_process	mitotic intra-S DNA damage checkpoint signaling
H	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
H	0051301	biological_process	cell division
H	0051865	biological_process	protein autoubiquitination
H	0061630	molecular_function	ubiquitin protein ligase activity
H	0061631	molecular_function	ubiquitin conjugating enzyme activity
H	0071406	biological_process	cellular response to methylmercury

Functional Information from PDB Data

site_id	AC1
Number of Residues	18
Details	binding site for residue ATP A 1101

Chain	Residue
A	ARG21
A	LYS519
A	VAL520
A	ALA542
A	LEU543
A	ASP544
A	ASN545
A	ALA548
A	MG1102
A	HOH1201
A	GLY443
A	ALA444
A	ASP470
A	ASP472
A	ASN478
A	ARG481
A	GLN482
A	LYS494

---

site_id	AC2
Number of Residues	4
Details	binding site for residue MG A 1102

Chain	Residue
A	ASP544
A	ATP1101
A	HOH1201
A	HOH1203

---

site_id	AC3
Number of Residues	19
Details	binding site for residue ATP E 1101

Chain	Residue
E	ARG21
E	GLY443
E	ALA444
E	ASP470
E	ASP472
E	ASN478
E	ARG481
E	GLN482
E	LYS494
E	LYS519
E	VAL520
E	ALA542
E	LEU543
E	ASP544
E	ASN545
E	ALA548
E	MG1102
E	HOH1201
E	HOH1202

---

site_id	AC4
Number of Residues	4
Details	binding site for residue MG E 1102

Chain	Residue
E	ASP544
E	ATP1101
E	HOH1201
E	HOH1202

---

site_id	AC5
Number of Residues	17
Details	binding site for residue ATP C 1101

Chain	Residue
C	ARG21
C	GLY443
C	ALA444
C	ASP470
C	ASP472
C	ASN478
C	ARG481
C	GLN482
C	LYS494
C	LYS519
C	VAL520
C	ALA542
C	LEU543
C	ASP544
C	ASN545
C	MG1102
C	HOH1201

---

site_id	AC6
Number of Residues	4
Details	binding site for residue MG C 1102

Chain	Residue
C	ASP544
C	ATP1101
C	HOH1201
C	HOH1202

---

site_id	AC7
Number of Residues	18
Details	binding site for residue ATP G 1101

Chain	Residue
G	ARG21
G	GLY443
G	ALA444
G	ASP470
G	ASP472
G	ASN478
G	ARG481
G	GLN482
G	LYS494
G	LYS519
G	VAL520
G	ALA542
G	LEU543
G	ASP544
G	ASN545
G	ALA548
G	MG1102
G	HOH1201

---

site_id	AC8
Number of Residues	4
Details	binding site for residue MG G 1102

Chain	Residue
G	ASP544
G	ATP1101
G	HOH1201
G	HOH1202

---

Functional Information from PROSITE/UniProt

site_id	PS00183
Number of Residues	16
Details	UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNVyrd.GrLCIsiL

Chain	Residue	Details
B	TYR84-LEU99

---

site_id	PS00536
Number of Residues	9
Details	UBIQUITIN_ACTIVAT_1 Ubiquitin-activating enzyme signature 1. KACSGKFtP

Chain	Residue	Details
A	LYS376-PRO384

---

site_id	PS00865
Number of Residues	9
Details	UBIQUITIN_ACTIVAT_2 Ubiquitin-activating enzyme active site. PLCTLRsFP

Chain	Residue	Details
A	PRO598-PRO606

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	648
Details	Domain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	548
Details	Repeat: {"description":"1-1"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	616
Details	Repeat: {"description":"1-2"}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2208
Details	Region: {"description":"2 approximate repeats"}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10132","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"24816100","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	28
Details	Binding site: {"evidences":[{"source":"PubMed","id":"35970836","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7ZH9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	20
Details	Binding site: {"evidences":[{"source":"PubMed","id":"35970836","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24816100","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"7ZH9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	12
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

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	6
Details	M-CSA 307

Chain	Residue	Details
E	ARG21	electrostatic stabiliser, hydrogen bond donor, steric role
E	ARG481	electrostatic stabiliser, hydrogen bond donor, steric role
E	ASP544	steric role
E	CYS600	activator, covalently attached, hydrogen bond donor, nucleophile, proton donor
E	THR601	hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay
E	ARG603	electrostatic stabiliser, hydrogen bond donor

---

site_id	MCSA2
Number of Residues	3
Details	M-CSA 939

Chain	Residue	Details
E	CYS600	nucleofuge
E	THR601	modifies pKa
E	ARG603	electrostatic stabiliser

---

site_id	MCSA3
Number of Residues	6
Details	M-CSA 307

Chain	Residue	Details
F	ASP21	electrostatic stabiliser, hydrogen bond donor, steric role

---

site_id	MCSA4
Number of Residues	3
Details	M-CSA 939

Chain

Residue

Details

---

site_id	MCSA5
Number of Residues	6
Details	M-CSA 307

Chain	Residue	Details
G	ARG21	electrostatic stabiliser, hydrogen bond donor, steric role
G	ARG481	electrostatic stabiliser, hydrogen bond donor, steric role
G	ASP544	steric role
G	CYS600	activator, covalently attached, hydrogen bond donor, nucleophile, proton donor
G	THR601	hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay
G	ARG603	electrostatic stabiliser, hydrogen bond donor

---

site_id	MCSA6
Number of Residues	3
Details	M-CSA 939

Chain	Residue	Details
G	CYS600	nucleofuge
G	THR601	modifies pKa
G	ARG603	electrostatic stabiliser

---

site_id	MCSA7
Number of Residues	6
Details	M-CSA 307

Chain	Residue	Details
H	ASP21	electrostatic stabiliser, hydrogen bond donor, steric role

---

site_id	MCSA8
Number of Residues	3
Details	M-CSA 939

Chain

Residue

Details

---