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2W9C
Asym. Unit
Info
Asym.Unit (149 KB)
Biol.Unit 1 (72 KB)
Biol.Unit 2 (71 KB)
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(1)
Title
:
TERNARY COMPLEX OF DPO4 BOUND TO N2,N2-DIMETHYL-DEOXYGUANOSINE MODIFIED DNA WITH INCOMING DTTP
Authors
:
R. L. Eoff, H. Zhang, I. D. Kosekov, C. J. Rizzo, M. Egli, F. P. Guengerich
Date
:
22 Jan 09 (Deposition) - 12 May 09 (Release) - 30 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.87
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,E (1x)
Biol. Unit 2: B,D,F (1x)
Keywords
:
Dna-Directed Dna Polymerase, N2-Dimethyl-G, Metal-Binding, Mutator Protein, Dna Damage, Dna Repair, Dna-Binding, Transferase, Dna Replication, Nucleotidyltransferase, Transferase/Dna, Dna, Dpo4, Adduct, Cytoplasm, Magnesium, Polymerase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
H. Zhang, R. L. Eoff, I. D. Kosekov, C. J. Rizzo, M. Egli, F. P. Guengerich
Structure-Function Relationships In Miscoding By Sulfolobus Solfataricus Dna Polymerase Dpo4: Guanine N2, N2-Dimethyl Substitution Produces Inactive And Miscoding Polymerase Complexes.
J. Biol. Chem. V. 284 17687 2009
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Hetero Components
(4, 12)
Info
All Hetero Components
1a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
1b: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
3a: 2'-DEOXY-N,N-DIMETHYL-5'-O-[OXIDO(... (O2Ga)
3b: 2'-DEOXY-N,N-DIMETHYL-5'-O-[OXIDO(... (O2Gb)
4a: THYMIDINE-5'-TRIPHOSPHATE (TTPa)
4b: THYMIDINE-5'-TRIPHOSPHATE (TTPb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
DOC
2
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
2
MG
6
Ligand/Ion
MAGNESIUM ION
3
O2G
2
Mod. Nucleotide
2'-DEOXY-N,N-DIMETHYL-5'-O-[OXIDO(OXO)PHOSPHONIO]GUANOSINE
4
TTP
2
Ligand/Ion
THYMIDINE-5'-TRIPHOSPHATE
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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
ASP A:105 , GLU A:106 , TTP A:1345 , HOH A:2021
BINDING SITE FOR RESIDUE MG A1342
2
AC2
SOFTWARE
ASP A:7 , PHE A:8 , ASP A:105 , TTP A:1345
BINDING SITE FOR RESIDUE MG A1343
3
AC3
SOFTWARE
ALA A:181 , ILE A:186 , HOH A:2029 , HOH A:2030 , DOC C:13
BINDING SITE FOR RESIDUE MG A1344
4
AC4
SOFTWARE
SER B:103 , ASP B:105 , GLU B:106 , HOH B:2015 , HOH B:2039
BINDING SITE FOR RESIDUE MG B1342
5
AC5
SOFTWARE
ASP B:7 , TTP B:1345 , HOH B:2001 , HOH B:2036 , HOH B:2037 , HOH B:2038
BINDING SITE FOR RESIDUE MG B1343
6
AC6
SOFTWARE
ALA B:181 , ASP B:182 , HOH B:2024 , HOH B:2025
BINDING SITE FOR RESIDUE MG B1344
7
AC7
SOFTWARE
ASP A:7 , PHE A:8 , ASP A:9 , TYR A:10 , PHE A:11 , THR A:45 , ARG A:51 , ALA A:57 , ASP A:105 , LYS A:159 , MG A:1342 , MG A:1343 , HOH A:2043 , DOC C:13 , O2G E:5 , DG E:6
BINDING SITE FOR RESIDUE TTP A1345
8
AC8
SOFTWARE
ASP B:7 , PHE B:8 , TYR B:10 , PHE B:11 , ALA B:44 , ARG B:51 , ALA B:57 , ASP B:105 , LYS B:159 , MG B:1343 , HOH B:2001 , HOH B:2036 , HOH B:2037 , HOH B:2038 , HOH B:2039 , HOH B:2040 , DOC D:13 , O2G F:5 , DG F:6
BINDING SITE FOR RESIDUE TTP B1345
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:3-187,B:3-187)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
DPO4_SULSO
3-187
2
A:3-187
B:3-187
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Exons
(0, 0)
Info
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2w9ca2 (A:241-342)
1b: SCOP_d2w9cb2 (B:241-342)
2a: SCOP_d2w9ca1 (A:1-240)
2b: SCOP_d2w9cb1 (B:1-240)
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Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Superfamily
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Family
:
automated matches
(41)
Protein domain
:
automated matches
(41)
Sulfolobus solfataricus [TaxId: 273057]
(31)
1a
d2w9ca2
A:241-342
1b
d2w9cb2
B:241-342
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
Lesion bypass DNA polymerase (Y-family), catalytic domain
(104)
Protein domain
:
automated matches
(35)
Sulfolobus solfataricus [TaxId: 273057]
(26)
2a
d2w9ca1
A:1-240
2b
d2w9cb1
B:1-240
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_IMS_HHH_2w9cB01 (B:168-199)
1b: PFAM_IMS_HHH_2w9cB02 (B:168-199)
2a: PFAM_IMS_2w9cB03 (B:6-156)
2b: PFAM_IMS_2w9cB04 (B:6-156)
3a: PFAM_IMS_C_2w9cB05 (B:211-334)
3b: PFAM_IMS_C_2w9cB06 (B:211-334)
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Clan
:
HHH
(112)
Family
:
IMS_HHH
(56)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(51)
1a
IMS_HHH-2w9cB01
B:168-199
1b
IMS_HHH-2w9cB02
B:168-199
Clan
:
no clan defined [family: IMS]
(76)
Family
:
IMS
(76)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(51)
2a
IMS-2w9cB03
B:6-156
2b
IMS-2w9cB04
B:6-156
Clan
:
no clan defined [family: IMS_C]
(74)
Family
:
IMS_C
(74)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(51)
3a
IMS_C-2w9cB05
B:211-334
3b
IMS_C-2w9cB06
B:211-334
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Asym.Unit (149 KB)
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