4ERP

Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide reductase complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003824	molecular_function	catalytic activity
A	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005829	cellular_component	cytosol
A	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
A	0006457	biological_process	protein folding
A	0009185	biological_process	ribonucleoside diphosphate metabolic process
A	0009263	biological_process	deoxyribonucleotide biosynthetic process
A	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
A	0015949	biological_process	nucleobase-containing small molecule interconversion
A	0016491	molecular_function	oxidoreductase activity
A	0042802	molecular_function	identical protein binding
A	0044183	molecular_function	protein folding chaperone
B	0000166	molecular_function	nucleotide binding
B	0003824	molecular_function	catalytic activity
B	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005829	cellular_component	cytosol
B	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
B	0006457	biological_process	protein folding
B	0009185	biological_process	ribonucleoside diphosphate metabolic process
B	0009263	biological_process	deoxyribonucleotide biosynthetic process
B	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
B	0015949	biological_process	nucleobase-containing small molecule interconversion
B	0016491	molecular_function	oxidoreductase activity
B	0042802	molecular_function	identical protein binding
B	0044183	molecular_function	protein folding chaperone
C	0000166	molecular_function	nucleotide binding
C	0003824	molecular_function	catalytic activity
C	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005829	cellular_component	cytosol
C	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
C	0006457	biological_process	protein folding
C	0009185	biological_process	ribonucleoside diphosphate metabolic process
C	0009263	biological_process	deoxyribonucleotide biosynthetic process
C	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
C	0015949	biological_process	nucleobase-containing small molecule interconversion
C	0016491	molecular_function	oxidoreductase activity
C	0042802	molecular_function	identical protein binding
C	0044183	molecular_function	protein folding chaperone
D	0000166	molecular_function	nucleotide binding
D	0003824	molecular_function	catalytic activity
D	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005829	cellular_component	cytosol
D	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
D	0006457	biological_process	protein folding
D	0009185	biological_process	ribonucleoside diphosphate metabolic process
D	0009263	biological_process	deoxyribonucleotide biosynthetic process
D	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
D	0015949	biological_process	nucleobase-containing small molecule interconversion
D	0016491	molecular_function	oxidoreductase activity
D	0042802	molecular_function	identical protein binding
D	0044183	molecular_function	protein folding chaperone
E	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
E	0005506	molecular_function	iron ion binding
E	0005515	molecular_function	protein binding
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
E	0009185	biological_process	ribonucleoside diphosphate metabolic process
E	0009263	biological_process	deoxyribonucleotide biosynthetic process
E	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
E	0015949	biological_process	nucleobase-containing small molecule interconversion
E	0016491	molecular_function	oxidoreductase activity
E	0042802	molecular_function	identical protein binding
E	0046872	molecular_function	metal ion binding
F	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
F	0005506	molecular_function	iron ion binding
F	0005515	molecular_function	protein binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
F	0009185	biological_process	ribonucleoside diphosphate metabolic process
F	0009263	biological_process	deoxyribonucleotide biosynthetic process
F	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
F	0015949	biological_process	nucleobase-containing small molecule interconversion
F	0016491	molecular_function	oxidoreductase activity
F	0042802	molecular_function	identical protein binding
F	0046872	molecular_function	metal ion binding
G	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
G	0005506	molecular_function	iron ion binding
G	0005515	molecular_function	protein binding
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
G	0009185	biological_process	ribonucleoside diphosphate metabolic process
G	0009263	biological_process	deoxyribonucleotide biosynthetic process
G	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
G	0015949	biological_process	nucleobase-containing small molecule interconversion
G	0016491	molecular_function	oxidoreductase activity
G	0042802	molecular_function	identical protein binding
G	0046872	molecular_function	metal ion binding
H	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
H	0005506	molecular_function	iron ion binding
H	0005515	molecular_function	protein binding
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
H	0009185	biological_process	ribonucleoside diphosphate metabolic process
H	0009263	biological_process	deoxyribonucleotide biosynthetic process
H	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
H	0015949	biological_process	nucleobase-containing small molecule interconversion
H	0016491	molecular_function	oxidoreductase activity
H	0042802	molecular_function	identical protein binding
H	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ATP A 801

Chain	Residue
A	VAL7
A	ILE22
A	VAL25
A	THR55
A	HIS59
A	PHE87
A	LYS91
A	LYS9
A	ARG10
A	ASP11
A	GLU15
A	ARG16
A	ILE17
A	ASN18
A	LYS21

---

site_id	AC2
Number of Residues	14
Details	BINDING SITE FOR RESIDUE ATP B 801

Chain	Residue
B	VAL7
B	LYS9
B	ARG10
B	ASP11
B	GLU15
B	ARG16
B	ASN18
B	LYS21
B	ILE22
B	VAL25
B	THR55
B	HIS59
B	PHE87
B	LYS91

---

site_id	AC3
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ATP C 801

Chain	Residue
C	VAL7
C	LYS9
C	ARG10
C	ASP11
C	GLU15
C	ARG16
C	ILE17
C	ASN18
C	LYS21
C	ILE22
C	VAL25
C	THR55
C	HIS59
C	PHE87
C	LYS91

---

site_id	AC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE ATP D 801

Chain	Residue
D	VAL7
D	LYS9
D	ARG10
D	ASP11
D	GLU15
D	ARG16
D	ILE17
D	ASN18
D	LYS21
D	ILE22
D	VAL25
D	THR55
D	HIS59
D	PHE87
D	LYS91

---

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FEO E 501

Chain	Residue
E	ASP84
E	GLU115
E	HIS118
E	GLU204
E	GLU238
E	HIS241
E	HOH601
E	HOH602

---

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FEO F 501

Chain	Residue
F	ASP84
F	GLU115
F	HIS118
F	GLU204
F	GLU238
F	HIS241
F	HOH601
F	HOH602

---

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FEO G 501

Chain	Residue
G	ASP84
G	GLU115
G	HIS118
G	GLU204
G	GLU238
G	HIS241
G	HOH601
G	HOH602

---

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FEO H 501

Chain	Residue
H	ASP84
H	GLU115
H	HIS118
H	GLU204
H	GLU238
H	HIS241
H	HOH601
H	HOH602

---

Functional Information from PROSITE/UniProt

site_id	PS00089
Number of Residues	23
Details	RIBORED_LARGE Ribonucleotide reductase large subunit signature. WeaLresikthGLRNstlSAlmP

Chain	Residue	Details
A	TRP599-PRO621

---

site_id	PS00368
Number of Residues	17
Details	RIBORED_SMALL Ribonucleotide reductase small subunit signature. SEt.IHSrSYthIirnIV

Chain	Residue	Details
E	SER114-VAL130

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	360
Details	Domain: {"description":"ATP-cone","evidences":[{"source":"PROSITE-ProRule","id":"PRU00492","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	8
Details	Active site: {"description":"Proton acceptor"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Active site: {"description":"Cysteine radical intermediate"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9309223","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3R1R","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9309223","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4R1R","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	8
Details	Site: {"description":"Important for hydrogen atom transfer"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	8
Details	Site: {"description":"Important for electron transfer"}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Active site: {}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	24
Details	Binding site: {}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	2
Details	M-CSA 918

Chain	Residue	Details
E	TYR122	pi-pi interaction, single electron relay
E	ASP237
A	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
A	GLU441	proton acceptor
A	CYS462
A	TYR730	pi-pi interaction, single electron relay
A	TYR731	pi-pi interaction, single electron relay

---

site_id	MCSA2
Number of Residues	2
Details	M-CSA 918

Chain	Residue	Details
F	TYR122	pi-pi interaction, single electron relay
F	ASP237
B	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
B	GLU441	proton acceptor
B	CYS462
B	TYR730	pi-pi interaction, single electron relay
B	TYR731	pi-pi interaction, single electron relay

---

site_id	MCSA3
Number of Residues	2
Details	M-CSA 918

Chain	Residue	Details
G	TYR122	pi-pi interaction, single electron relay
G	ASP237
C	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
C	GLU441	proton acceptor
C	CYS462
C	TYR730	pi-pi interaction, single electron relay
C	TYR731	pi-pi interaction, single electron relay

---

site_id	MCSA4
Number of Residues	2
Details	M-CSA 918

Chain	Residue	Details
H	TYR122	pi-pi interaction, single electron relay
H	ASP237
D	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
D	GLU441	proton acceptor
D	CYS462
D	TYR730	pi-pi interaction, single electron relay
D	TYR731	pi-pi interaction, single electron relay

---