6YL3

High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
0	0035550	cellular_component	urease complex
0	0043419	biological_process	urea catabolic process
1	0005737	cellular_component	cytoplasm
1	0009039	molecular_function	urease activity
1	0016151	molecular_function	nickel cation binding
1	0016787	molecular_function	hydrolase activity
1	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
1	0019627	biological_process	urea metabolic process
1	0043419	biological_process	urea catabolic process
1	0046872	molecular_function	metal ion binding
2	0005737	cellular_component	cytoplasm
2	0009039	molecular_function	urease activity
2	0016151	molecular_function	nickel cation binding
2	0016787	molecular_function	hydrolase activity
2	0019627	biological_process	urea metabolic process
2	0043419	biological_process	urea catabolic process
3	0035550	cellular_component	urease complex
3	0043419	biological_process	urea catabolic process
4	0005737	cellular_component	cytoplasm
4	0009039	molecular_function	urease activity
4	0016151	molecular_function	nickel cation binding
4	0016787	molecular_function	hydrolase activity
4	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
4	0019627	biological_process	urea metabolic process
4	0043419	biological_process	urea catabolic process
4	0046872	molecular_function	metal ion binding
5	0005737	cellular_component	cytoplasm
5	0009039	molecular_function	urease activity
5	0016151	molecular_function	nickel cation binding
5	0016787	molecular_function	hydrolase activity
5	0019627	biological_process	urea metabolic process
5	0043419	biological_process	urea catabolic process
6	0035550	cellular_component	urease complex
6	0043419	biological_process	urea catabolic process
7	0005737	cellular_component	cytoplasm
7	0009039	molecular_function	urease activity
7	0016151	molecular_function	nickel cation binding
7	0016787	molecular_function	hydrolase activity
7	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
7	0019627	biological_process	urea metabolic process
7	0043419	biological_process	urea catabolic process
7	0046872	molecular_function	metal ion binding
8	0005737	cellular_component	cytoplasm
8	0009039	molecular_function	urease activity
8	0016151	molecular_function	nickel cation binding
8	0016787	molecular_function	hydrolase activity
8	0019627	biological_process	urea metabolic process
8	0043419	biological_process	urea catabolic process
9	0035550	cellular_component	urease complex
9	0043419	biological_process	urea catabolic process
A	0005737	cellular_component	cytoplasm
A	0009039	molecular_function	urease activity
A	0016151	molecular_function	nickel cation binding
A	0016787	molecular_function	hydrolase activity
A	0019627	biological_process	urea metabolic process
A	0043419	biological_process	urea catabolic process
B	0035550	cellular_component	urease complex
B	0043419	biological_process	urea catabolic process
C	0005737	cellular_component	cytoplasm
C	0009039	molecular_function	urease activity
C	0016151	molecular_function	nickel cation binding
C	0016787	molecular_function	hydrolase activity
C	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
C	0019627	biological_process	urea metabolic process
C	0043419	biological_process	urea catabolic process
C	0046872	molecular_function	metal ion binding
D	0005737	cellular_component	cytoplasm
D	0009039	molecular_function	urease activity
D	0016151	molecular_function	nickel cation binding
D	0016787	molecular_function	hydrolase activity
D	0019627	biological_process	urea metabolic process
D	0043419	biological_process	urea catabolic process
E	0035550	cellular_component	urease complex
E	0043419	biological_process	urea catabolic process
F	0005737	cellular_component	cytoplasm
F	0009039	molecular_function	urease activity
F	0016151	molecular_function	nickel cation binding
F	0016787	molecular_function	hydrolase activity
F	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
F	0019627	biological_process	urea metabolic process
F	0043419	biological_process	urea catabolic process
F	0046872	molecular_function	metal ion binding
G	0005737	cellular_component	cytoplasm
G	0009039	molecular_function	urease activity
G	0016151	molecular_function	nickel cation binding
G	0016787	molecular_function	hydrolase activity
G	0019627	biological_process	urea metabolic process
G	0043419	biological_process	urea catabolic process
H	0035550	cellular_component	urease complex
H	0043419	biological_process	urea catabolic process
I	0005737	cellular_component	cytoplasm
I	0009039	molecular_function	urease activity
I	0016151	molecular_function	nickel cation binding
I	0016787	molecular_function	hydrolase activity
I	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
I	0019627	biological_process	urea metabolic process
I	0043419	biological_process	urea catabolic process
I	0046872	molecular_function	metal ion binding
J	0005737	cellular_component	cytoplasm
J	0009039	molecular_function	urease activity
J	0016151	molecular_function	nickel cation binding
J	0016787	molecular_function	hydrolase activity
J	0019627	biological_process	urea metabolic process
J	0043419	biological_process	urea catabolic process
K	0035550	cellular_component	urease complex
K	0043419	biological_process	urea catabolic process
L	0005737	cellular_component	cytoplasm
L	0009039	molecular_function	urease activity
L	0016151	molecular_function	nickel cation binding
L	0016787	molecular_function	hydrolase activity
L	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
L	0019627	biological_process	urea metabolic process
L	0043419	biological_process	urea catabolic process
L	0046872	molecular_function	metal ion binding
M	0005737	cellular_component	cytoplasm
M	0009039	molecular_function	urease activity
M	0016151	molecular_function	nickel cation binding
M	0016787	molecular_function	hydrolase activity
M	0019627	biological_process	urea metabolic process
M	0043419	biological_process	urea catabolic process
N	0035550	cellular_component	urease complex
N	0043419	biological_process	urea catabolic process
O	0005737	cellular_component	cytoplasm
O	0009039	molecular_function	urease activity
O	0016151	molecular_function	nickel cation binding
O	0016787	molecular_function	hydrolase activity
O	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
O	0019627	biological_process	urea metabolic process
O	0043419	biological_process	urea catabolic process
O	0046872	molecular_function	metal ion binding
P	0005737	cellular_component	cytoplasm
P	0009039	molecular_function	urease activity
P	0016151	molecular_function	nickel cation binding
P	0016787	molecular_function	hydrolase activity
P	0019627	biological_process	urea metabolic process
P	0043419	biological_process	urea catabolic process
Q	0035550	cellular_component	urease complex
Q	0043419	biological_process	urea catabolic process
R	0005737	cellular_component	cytoplasm
R	0009039	molecular_function	urease activity
R	0016151	molecular_function	nickel cation binding
R	0016787	molecular_function	hydrolase activity
R	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
R	0019627	biological_process	urea metabolic process
R	0043419	biological_process	urea catabolic process
R	0046872	molecular_function	metal ion binding
S	0005737	cellular_component	cytoplasm
S	0009039	molecular_function	urease activity
S	0016151	molecular_function	nickel cation binding
S	0016787	molecular_function	hydrolase activity
S	0019627	biological_process	urea metabolic process
S	0043419	biological_process	urea catabolic process
T	0035550	cellular_component	urease complex
T	0043419	biological_process	urea catabolic process
U	0005737	cellular_component	cytoplasm
U	0009039	molecular_function	urease activity
U	0016151	molecular_function	nickel cation binding
U	0016787	molecular_function	hydrolase activity
U	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
U	0019627	biological_process	urea metabolic process
U	0043419	biological_process	urea catabolic process
U	0046872	molecular_function	metal ion binding
V	0005737	cellular_component	cytoplasm
V	0009039	molecular_function	urease activity
V	0016151	molecular_function	nickel cation binding
V	0016787	molecular_function	hydrolase activity
V	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
V	0019627	biological_process	urea metabolic process
V	0043419	biological_process	urea catabolic process
V	0046872	molecular_function	metal ion binding
W	0005737	cellular_component	cytoplasm
W	0009039	molecular_function	urease activity
W	0016151	molecular_function	nickel cation binding
W	0016787	molecular_function	hydrolase activity
W	0019627	biological_process	urea metabolic process
W	0043419	biological_process	urea catabolic process
X	0035550	cellular_component	urease complex
X	0043419	biological_process	urea catabolic process
Y	0005737	cellular_component	cytoplasm
Y	0009039	molecular_function	urease activity
Y	0016151	molecular_function	nickel cation binding
Y	0016787	molecular_function	hydrolase activity
Y	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Y	0019627	biological_process	urea metabolic process
Y	0043419	biological_process	urea catabolic process
Y	0046872	molecular_function	metal ion binding
Z	0005737	cellular_component	cytoplasm
Z	0009039	molecular_function	urease activity
Z	0016151	molecular_function	nickel cation binding
Z	0016787	molecular_function	hydrolase activity
Z	0019627	biological_process	urea metabolic process
Z	0043419	biological_process	urea catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue NI C 601

Chain	Residue
C	HIS139
C	KCX222
C	HIS251
C	HIS277
C	NI602
C	HOH735

---

site_id	AC2
Number of Residues	5
Details	binding site for residue NI C 602

Chain	Residue
C	ASP365
C	NI601
C	HIS139
C	HIS141
C	KCX222

---

site_id	AC3
Number of Residues	6
Details	binding site for residue NI F 601

Chain	Residue
F	HIS139
F	KCX222
F	HIS251
F	HIS277
F	NI602
F	HOH733

---

site_id	AC4
Number of Residues	5
Details	binding site for residue NI F 602

Chain	Residue
F	HIS139
F	HIS141
F	KCX222
F	ASP365
F	NI601

---

site_id	AC5
Number of Residues	6
Details	binding site for residue NI I 601

Chain	Residue
I	HIS139
I	KCX222
I	HIS251
I	HIS277
I	NI602
I	HOH731

---

site_id	AC6
Number of Residues	5
Details	binding site for residue NI I 602

Chain	Residue
I	HIS139
I	HIS141
I	KCX222
I	ASP365
I	NI601

---

site_id	AC7
Number of Residues	6
Details	binding site for residue NI L 601

Chain	Residue
L	HIS139
L	KCX222
L	HIS251
L	HIS277
L	NI602
L	HOH734

---

site_id	AC8
Number of Residues	5
Details	binding site for residue NI L 602

Chain	Residue
L	HIS139
L	HIS141
L	KCX222
L	ASP365
L	NI601

---

site_id	AC9
Number of Residues	6
Details	binding site for residue NI O 601

Chain	Residue
O	HIS139
O	KCX222
O	HIS251
O	HIS277
O	NI602
O	HOH732

---

site_id	AD1
Number of Residues	5
Details	binding site for residue NI O 602

Chain	Residue
O	HIS139
O	HIS141
O	KCX222
O	ASP365
O	NI601

---

site_id	AD2
Number of Residues	6
Details	binding site for residue NI R 601

Chain	Residue
R	HIS139
R	KCX222
R	HIS251
R	HIS277
R	NI602
R	HOH735

---

site_id	AD3
Number of Residues	5
Details	binding site for residue NI R 602

Chain	Residue
R	HIS139
R	HIS141
R	KCX222
R	ASP365
R	NI601

---

site_id	AD4
Number of Residues	6
Details	binding site for residue NI V 601

Chain	Residue
V	HIS139
V	KCX222
V	HIS251
V	HIS277
V	NI602
V	HOH733

---

site_id	AD5
Number of Residues	5
Details	binding site for residue NI V 602

Chain	Residue
V	HIS139
V	HIS141
V	KCX222
V	ASP365
V	NI601

---

site_id	AD6
Number of Residues	6
Details	binding site for residue NI Y 601

Chain	Residue
Y	HIS139
Y	KCX222
Y	HIS251
Y	HIS277
Y	NI602
Y	HOH731

---

site_id	AD7
Number of Residues	5
Details	binding site for residue NI Y 602

Chain	Residue
Y	HIS139
Y	HIS141
Y	KCX222
Y	ASP365
Y	NI601

---

site_id	AD8
Number of Residues	6
Details	binding site for residue NI 1 601

Chain	Residue
1	HIS139
1	KCX222
1	HIS251
1	HIS277
1	NI602
1	HOH730

---

site_id	AD9
Number of Residues	5
Details	binding site for residue NI 1 602

Chain	Residue
1	HIS139
1	HIS141
1	KCX222
1	ASP365
1	NI601

---

site_id	AE1
Number of Residues	6
Details	binding site for residue NI 4 601

Chain	Residue
4	HIS139
4	KCX222
4	HIS251
4	HIS277
4	NI602
4	HOH734

---

site_id	AE2
Number of Residues	5
Details	binding site for residue NI 4 602

Chain	Residue
4	HIS139
4	HIS141
4	KCX222
4	ASP365
4	NI601

---

site_id	AE3
Number of Residues	6
Details	binding site for residue NI 7 601

Chain	Residue
7	HIS139
7	KCX222
7	HIS251
7	HIS277
7	NI602
7	HOH731

---

site_id	AE4
Number of Residues	5
Details	binding site for residue NI 7 602

Chain	Residue
7	HIS139
7	HIS141
7	KCX222
7	ASP365
7	NI601

---

site_id	AE5
Number of Residues	6
Details	binding site for residue NI U 601

Chain	Residue
U	HIS139
U	KCX222
U	HIS251
U	HIS277
U	NI602
U	HOH735

---

site_id	AE6
Number of Residues	5
Details	binding site for residue NI U 602

Chain	Residue
U	HIS139
U	HIS141
U	KCX222
U	ASP365
U	NI601

---

Functional Information from PROSITE/UniProt

site_id	PS00145
Number of Residues	17
Details	UREASE_2 Urease active site. MVCHNLnpnVpaDVsFA

Chain	Residue	Details
1	MET322-ALA338

---

site_id	PS01120
Number of Residues	14
Details	UREASE_1 Urease nickel ligands signature. TAAGIDtHIHlisP

Chain	Residue	Details
1	THR132-PRO145

---