5CNV
Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to GDP and TTP at 3.20 Angstroms resolution
Functional Information from GO Data
Chain | GOid | namespace | contents |
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 | 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 | 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 | 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 | 18 |
Details | binding site for residue GDP A 801 |
Chain | Residue |
A | THR209 |
A | CYS439 |
A | GLU441 |
A | LEU464 |
A | MET620 |
A | PRO621 |
A | SER622 |
A | GLU623 |
A | THR624 |
A | SER625 |
A | SER224 |
A | CYS225 |
A | ALA252 |
A | GLY253 |
A | ARG298 |
A | GLY299 |
A | ASN437 |
A | LEU438 |
site_id | AC2 |
Number of Residues | 16 |
Details | binding site for residue DAT A 802 |
Chain | Residue |
A | VAL7 |
A | LYS9 |
A | ARG10 |
A | GLU15 |
A | ARG16 |
A | ILE17 |
A | ASN18 |
A | LYS21 |
A | VAL25 |
A | THR55 |
A | HIS59 |
A | PHE87 |
A | LYS91 |
A | MG803 |
A | TTP804 |
A | HOH901 |
site_id | AC3 |
Number of Residues | 3 |
Details | binding site for residue MG A 803 |
Chain | Residue |
A | DAT802 |
A | TTP804 |
A | HOH901 |
site_id | AC4 |
Number of Residues | 10 |
Details | binding site for residue TTP A 804 |
Chain | Residue |
A | LYS9 |
A | LYS21 |
A | ARG24 |
A | VAL25 |
A | TRP28 |
A | LYS91 |
A | PHE97 |
A | DAT802 |
A | MG803 |
A | HOH901 |
site_id | AC5 |
Number of Residues | 14 |
Details | binding site for residue TTP A 805 |
Chain | Residue |
A | ASP232 |
A | SER233 |
A | LEU234 |
A | ARG262 |
A | ILE268 |
A | ARG269 |
A | HIS275 |
A | MG806 |
A | HOH905 |
A | HOH906 |
A | HOH907 |
A | HOH908 |
B | SER249 |
B | CYS292 |
site_id | AC6 |
Number of Residues | 4 |
Details | binding site for residue MG A 806 |
Chain | Residue |
A | TTP805 |
A | HOH905 |
A | HOH906 |
A | HOH907 |
site_id | AC7 |
Number of Residues | 18 |
Details | binding site for residue GDP B 801 |
Chain | Residue |
B | PRO208 |
B | THR209 |
B | SER224 |
B | CYS225 |
B | ALA252 |
B | GLY253 |
B | ARG298 |
B | GLY299 |
B | ASN437 |
B | LEU438 |
B | CYS439 |
B | GLU441 |
B | MET620 |
B | PRO621 |
B | SER622 |
B | GLU623 |
B | THR624 |
B | SER625 |
site_id | AC8 |
Number of Residues | 17 |
Details | binding site for residue DAT B 802 |
Chain | Residue |
B | HOH901 |
B | VAL7 |
B | LYS9 |
B | ARG10 |
B | GLU15 |
B | ARG16 |
B | ILE17 |
B | ASN18 |
B | LYS21 |
B | ILE22 |
B | VAL25 |
B | THR55 |
B | HIS59 |
B | PHE87 |
B | LYS91 |
B | MG803 |
B | TTP804 |
site_id | AC9 |
Number of Residues | 3 |
Details | binding site for residue MG B 803 |
Chain | Residue |
B | DAT802 |
B | TTP804 |
B | HOH901 |
site_id | AD1 |
Number of Residues | 9 |
Details | binding site for residue TTP B 804 |
Chain | Residue |
B | LYS9 |
B | LYS21 |
B | ARG24 |
B | VAL25 |
B | TRP28 |
B | PHE97 |
B | DAT802 |
B | MG803 |
B | HOH901 |
site_id | AD2 |
Number of Residues | 14 |
Details | binding site for residue TTP B 805 |
Chain | Residue |
A | SER249 |
A | CYS292 |
B | ASP232 |
B | SER233 |
B | LEU234 |
B | ARG262 |
B | ILE268 |
B | ARG269 |
B | HIS275 |
B | PHE281 |
B | MG806 |
B | HOH903 |
B | HOH904 |
B | HOH905 |
site_id | AD3 |
Number of Residues | 4 |
Details | binding site for residue MG B 806 |
Chain | Residue |
B | TTP805 |
B | HOH903 |
B | HOH904 |
B | HOH905 |
site_id | AD4 |
Number of Residues | 20 |
Details | binding site for residue GDP C 801 |
Chain | Residue |
C | PRO208 |
C | THR209 |
C | SER224 |
C | CYS225 |
C | ALA252 |
C | GLY253 |
C | ARG298 |
C | GLY299 |
C | ASN437 |
C | LEU438 |
C | CYS439 |
C | GLU441 |
C | LEU464 |
C | MET620 |
C | PRO621 |
C | SER622 |
C | GLU623 |
C | THR624 |
C | SER625 |
C | HOH903 |
site_id | AD5 |
Number of Residues | 17 |
Details | binding site for residue DAT C 802 |
Chain | Residue |
C | LYS9 |
C | ARG10 |
C | GLU15 |
C | ARG16 |
C | ILE17 |
C | ASN18 |
C | LYS21 |
C | ILE22 |
C | VAL25 |
C | THR55 |
C | HIS59 |
C | ILE62 |
C | PHE87 |
C | LYS91 |
C | MG803 |
C | TTP804 |
C | HOH901 |
site_id | AD6 |
Number of Residues | 3 |
Details | binding site for residue MG C 803 |
Chain | Residue |
C | DAT802 |
C | TTP804 |
C | HOH901 |
site_id | AD7 |
Number of Residues | 9 |
Details | binding site for residue TTP C 804 |
Chain | Residue |
C | LYS9 |
C | LYS21 |
C | ARG24 |
C | VAL25 |
C | TRP28 |
C | PHE97 |
C | DAT802 |
C | MG803 |
C | HOH901 |
site_id | AD8 |
Number of Residues | 13 |
Details | binding site for residue TTP C 805 |
Chain | Residue |
C | ASP232 |
C | SER233 |
C | LEU234 |
C | ARG262 |
C | ILE268 |
C | ARG269 |
C | HIS275 |
C | MG806 |
C | HOH909 |
C | HOH910 |
C | HOH911 |
D | SER249 |
D | CYS292 |
site_id | AD9 |
Number of Residues | 4 |
Details | binding site for residue MG C 806 |
Chain | Residue |
C | TTP805 |
C | HOH909 |
C | HOH910 |
C | HOH911 |
site_id | AE1 |
Number of Residues | 19 |
Details | binding site for residue GDP D 801 |
Chain | Residue |
D | THR209 |
D | SER224 |
D | CYS225 |
D | ALA252 |
D | GLY253 |
D | ARG298 |
D | GLY299 |
D | ASN437 |
D | LEU438 |
D | CYS439 |
D | GLU441 |
D | LEU464 |
D | MET620 |
D | PRO621 |
D | SER622 |
D | GLU623 |
D | THR624 |
D | SER625 |
D | HOH904 |
site_id | AE2 |
Number of Residues | 16 |
Details | binding site for residue DAT D 802 |
Chain | Residue |
D | VAL7 |
D | LYS9 |
D | ARG10 |
D | GLU15 |
D | ARG16 |
D | ASN18 |
D | LYS21 |
D | ILE22 |
D | VAL25 |
D | THR55 |
D | HIS59 |
D | PHE87 |
D | LYS91 |
D | MG803 |
D | TTP804 |
D | HOH901 |
site_id | AE3 |
Number of Residues | 3 |
Details | binding site for residue MG D 803 |
Chain | Residue |
D | DAT802 |
D | TTP804 |
D | HOH901 |
site_id | AE4 |
Number of Residues | 9 |
Details | binding site for residue TTP D 804 |
Chain | Residue |
D | LYS9 |
D | LYS21 |
D | ARG24 |
D | VAL25 |
D | TRP28 |
D | PHE97 |
D | DAT802 |
D | MG803 |
D | HOH901 |
site_id | AE5 |
Number of Residues | 14 |
Details | binding site for residue TTP D 805 |
Chain | Residue |
C | SER249 |
C | CYS292 |
D | ASP232 |
D | SER233 |
D | LEU234 |
D | ARG262 |
D | ILE268 |
D | ARG269 |
D | HIS275 |
D | PHE281 |
D | MG806 |
D | HOH910 |
D | HOH911 |
D | HOH912 |
site_id | AE6 |
Number of Residues | 4 |
Details | binding site for residue MG D 806 |
Chain | Residue |
D | TTP805 |
D | HOH910 |
D | HOH911 |
D | HOH912 |
site_id | AE7 |
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 | HOH603 |
site_id | AE8 |
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 | AE9 |
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 | HOH603 |
site_id | AF1 |
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 | HOH603 |
H | HOH606 |
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 | 4 |
Details | ACT_SITE: |
Chain | Residue | Details |
E | TYR122 | |
F | TYR122 | |
G | TYR122 | |
H | TYR122 | |
C | ASN437 | |
C | GLU441 | |
D | ASN437 | |
D | GLU441 |
site_id | SWS_FT_FI2 |
Number of Residues | 24 |
Details | BINDING: |
Chain | Residue | Details |
E | ASP84 | |
F | GLU204 | |
F | GLU238 | |
F | HIS241 | |
G | ASP84 | |
G | GLU115 | |
G | HIS118 | |
G | GLU204 | |
G | GLU238 | |
G | HIS241 | |
H | ASP84 | |
E | GLU115 | |
H | GLU115 | |
H | HIS118 | |
H | GLU204 | |
H | GLU238 | |
H | HIS241 | |
E | HIS118 | |
E | GLU204 | |
E | GLU238 | |
E | HIS241 | |
F | ASP84 | |
F | GLU115 | |
F | HIS118 |
site_id | SWS_FT_FI3 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0000269|PubMed:9309223, ECO:0007744|PDB:3R1R |
Chain | Residue | Details |
A | LYS9 | |
C | GLU15 | |
C | THR55 | |
C | LYS91 | |
D | LYS9 | |
D | GLU15 | |
D | THR55 | |
D | LYS91 | |
A | GLU15 | |
A | THR55 | |
A | LYS91 | |
B | LYS9 | |
B | GLU15 | |
B | THR55 | |
B | LYS91 | |
C | LYS9 |
site_id | SWS_FT_FI4 |
Number of Residues | 28 |
Details | BINDING: BINDING => ECO:0000269|PubMed:9309223, ECO:0007744|PDB:4R1R |
Chain | Residue | Details |
A | THR209 | |
B | ARG262 | |
B | ARG269 | |
B | ASN437 | |
B | GLU441 | |
B | GLU623 | |
C | THR209 | |
C | ASP232 | |
C | ARG262 | |
C | ARG269 | |
C | ASN437 | |
A | ASP232 | |
C | GLU441 | |
C | GLU623 | |
D | THR209 | |
D | ASP232 | |
D | ARG262 | |
D | ARG269 | |
D | ASN437 | |
D | GLU441 | |
D | GLU623 | |
A | ARG262 | |
A | ARG269 | |
A | ASN437 | |
A | GLU441 | |
A | GLU623 | |
B | THR209 | |
B | ASP232 |
site_id | SWS_FT_FI5 |
Number of Residues | 8 |
Details | SITE: Important for hydrogen atom transfer |
Chain | Residue | Details |
A | CYS225 | |
A | CYS462 | |
B | CYS225 | |
B | CYS462 | |
C | CYS225 | |
C | CYS462 | |
D | CYS225 | |
D | CYS462 |
site_id | SWS_FT_FI6 |
Number of Residues | 8 |
Details | SITE: Important for electron transfer |
Chain | Residue | Details |
A | TYR730 | |
A | TYR731 | |
B | TYR730 | |
B | TYR731 | |
C | TYR730 | |
C | TYR731 | |
D | TYR730 | |
D | TYR731 |
site_id | SWS_FT_FI7 |
Number of Residues | 8 |
Details | SITE: Interacts with thioredoxin/glutaredoxin |
Chain | Residue | Details |
A | CYS754 | |
A | CYS759 | |
B | CYS754 | |
B | CYS759 | |
C | CYS754 | |
C | CYS759 | |
D | CYS754 | |
D | CYS759 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:18723842 |
Chain | Residue | Details |
A | LYS283 | |
B | LYS283 | |
C | LYS283 | |
D | LYS283 |
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 | 5 |
Details | M-CSA 918 |
Chain | Residue | Details |
G | GLU115 | |
G | TYR122 | pi-pi interaction, single electron relay |
G | ASP237 | |
G | GLU350 | |
G | TYR356 | |
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 |