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2BQ1
Asym. Unit
Info
Asym.Unit (319 KB)
Biol.Unit 1 (310 KB)
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(1)
Title
:
RIBONUCLEOTIDE REDUCTASE CLASS 1B HOLOCOMPLEX R1E,R2F FROM SALMONELLA TYPHIMURIUM
Authors
:
M. Uppsten, M. Farnegardh, V. Domkin, U. Uhlin
Date
:
26 Apr 05 (Deposition) - 17 May 06 (Release) - 18 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
4.00
Chains
:
Asym. Unit : E,F,I,J
Biol. Unit 1: E,F,I,J (1x)
Keywords
:
R1, R2, R1E, R2F, Iron, Class 1B, Holocomplex, Allosteric Regulation, Ribonucleotide Reductase, Atp-Binding, Metal- Binding, Oxidoreductase, Dna Replication, Radical Transfer, Allosteric Enzyme, Asymmetric Complex, Nucleotide-Binding
(Keyword Search:
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Reference
:
M. Uppsten, M. Farnegardh, V. Domkin, U. Uhlin
The First Holocomplex Structure Of Ribonucleotide Reductase Gives New Insight Into Its Mechanism Of Action
J. Mol. Biol. V. 359 365 2006
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTa)
1b: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTb)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
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Label:
No.
Name
Count
Type
Full Name
1
DGT
2
Ligand/Ion
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2
FE
4
Ligand/Ion
FE (III) ION
3
MG
2
Ligand/Ion
MAGNESIUM ION
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
DGT E:1700
BINDING SITE FOR RESIDUE MG E1701
2
AC2
SOFTWARE
DGT F:1700
BINDING SITE FOR RESIDUE MG F1701
3
AC3
SOFTWARE
ASP I:67 , GLU I:98 , HIS I:101 , PHE I:162 , GLU I:192
BINDING SITE FOR RESIDUE FE I1320
4
AC4
SOFTWARE
GLU I:98 , GLU I:158 , GLU I:192 , HIS I:195
BINDING SITE FOR RESIDUE FE I1321
5
AC5
SOFTWARE
ASP J:67 , GLU J:98 , HIS J:101 , GLU J:192 , FE J:1288
BINDING SITE FOR RESIDUE FE J1287
6
AC6
SOFTWARE
GLU J:98 , GLU J:158 , GLU J:192 , HIS J:195 , FE J:1287
BINDING SITE FOR RESIDUE FE J1288
7
AC7
SOFTWARE
ASP E:185 , ASN E:186 , MET E:187 , ILE E:190 , ARG E:215 , ILE E:221 , LYS E:222 , MG E:1701 , LYS F:202 , TYR F:244
BINDING SITE FOR RESIDUE DGT E1700
8
AC8
SOFTWARE
LYS E:202 , TYR E:244 , ASP F:185 , ASN F:186 , MET F:187 , ARG F:215 , ILE F:221 , LYS F:222 , MG F:1701
BINDING SITE FOR RESIDUE DGT F1700
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: RIBORED_SMALL (I:97-113,J:97-113)
2: RIBORED_LARGE (E:566-588,F:566-588)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBORED_SMALL
PS00368
Ribonucleotide reductase small subunit signature.
RIR4_SALTY
97-113
2
I:97-113
J:97-113
2
RIBORED_LARGE
PS00089
Ribonucleotide reductase large subunit signature.
RIR3_SALTY
566-588
2
E:566-588
F:566-588
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2bq1i1 (I:6-288)
1b: SCOP_d2bq1j1 (J:6-286)
2a: SCOP_d2bq1e1 (E:13-174)
2b: SCOP_d2bq1f1 (F:13-174)
3a: SCOP_d2bq1e2 (E:175-699)
3b: SCOP_d2bq1f2 (F:175-699)
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Classes
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Protein Domains
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Organisms
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)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ribonucleotide reductase-like
(185)
Protein domain
:
Ribonucleotide reductase R2
(45)
Salmonella typhimurium [TaxId: 90371]
(3)
1a
d2bq1i1
I:6-288
1b
d2bq1j1
J:6-286
Fold
:
R1 subunit of ribonucleotide reductase, N-terminal domain
(13)
Superfamily
:
R1 subunit of ribonucleotide reductase, N-terminal domain
(13)
Family
:
R1 subunit of ribonucleotide reductase, N-terminal domain
(13)
Protein domain
:
R1 subunit of ribonucleotide reductase, N-terminal domain
(13)
Salmonella typhimurium [TaxId: 90371]
(5)
2a
d2bq1e1
E:13-174
2b
d2bq1f1
F:13-174
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PFL-like glycyl radical enzymes
(32)
Superfamily
:
PFL-like glycyl radical enzymes
(32)
Family
:
R1 subunit of ribonucleotide reductase, C-terminal domain
(13)
Protein domain
:
R1 subunit of ribonucleotide reductase, C-terminal domain
(13)
Salmonella typhimurium [TaxId: 90371]
(5)
3a
d2bq1e2
E:175-699
3b
d2bq1f2
F:175-699
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2bq1I01 (I:6-288)
1b: CATH_2bq1J00 (J:6-286)
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Organisms
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)
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)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Ribonucleotide Reductase, subunit A
(86)
Homologous Superfamily
:
Ribonucleotide Reductase, subunit A
(86)
Salmonella typhimurium. Organism_taxid: 602.
(3)
1a
2bq1I01
I:6-288
1b
2bq1J00
J:6-286
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Pfam Domains
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Protein & NOT Site
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Chain E
Chain F
Chain I
Chain J
Asymmetric Unit 1
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Asym.Unit (319 KB)
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