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1XS4
Asym. Unit
Info
Asym.Unit (199 KB)
Biol.Unit 1 (97 KB)
Biol.Unit 2 (98 KB)
Biol.Unit 3 (189 KB)
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(1)
Title
:
DCTP DEAMINASE FROM ESCHERICHIA COLI- E138A MUTANT ENZYME IN COMPLEX WITH DCTP
Authors
:
E. Johansson, M. Fano, J. H. Bynck, J. Neuhard, S. Larsen, B. W. Sigurskjold, U. Christensen, M. Willemoes
Date
:
18 Oct 04 (Deposition) - 21 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.53
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Biol. Unit 3: A,B,C,D,E,F (1x)
Keywords
:
Dctp Deaminase, Nucleotide Metabolism, Trimer, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Johansson, M. Fano, J. H. Bynck, J. Neuhard, S. Larsen, B. W. Sigurskjold, U. Christensen, M. Willemoes
Structures Of Dctp Deaminase From Escherichia Coli With Bound Substrate And Product: Reaction Mechanism And Determinants Of Mono- And Bifunctionality For A Family Of Enzymes
J. Biol. Chem. V. 280 3051 2005
(for further references see the
PDB file header
)
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Hetero Components
(3, 36)
Info
All Hetero Components
1a: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPa)
1b: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPb)
1c: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPc)
1d: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPd)
1e: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPe)
1f: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCPf)
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: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DCP
6
Ligand/Ion
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2
MG
6
Ligand/Ion
MAGNESIUM ION
3
MSE
24
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
DCP A:1194 , HOH A:2200 , HOH A:2223
BINDING SITE FOR RESIDUE MG C 1195
02
AC2
SOFTWARE
HOH A:2222 , DCP B:2194 , HOH B:3221
BINDING SITE FOR RESIDUE MG A 2195
03
AC3
SOFTWARE
HOH B:3219 , DCP C:3194
BINDING SITE FOR RESIDUE MG B 3195
04
AC4
SOFTWARE
DCP D:4194 , HOH D:5208
BINDING SITE FOR RESIDUE MG F 4195
05
AC5
SOFTWARE
DCP E:5194 , HOH E:6216 , HOH E:6228
BINDING SITE FOR RESIDUE MG D 5195
06
AC6
SOFTWARE
DCP F:6194 , HOH F:6197 , HOH F:6212
BINDING SITE FOR RESIDUE MG E 6195
07
AC7
SOFTWARE
ALA A:124 , ARG A:126 , ASP A:128 , TRP A:131 , ILE A:135 , VAL A:136 , TYR A:171 , ARG A:174 , ALA A:177 , LYS A:178 , TYR A:179 , GLN A:182 , HOH A:2200 , HOH A:2219 , HOH A:2221 , HOH A:2223 , HOH A:2225 , HOH A:2231 , ARG C:110 , SER C:111 , SER C:112 , ARG C:115 , MG C:1195
BINDING SITE FOR RESIDUE DCP A 1194
08
AC8
SOFTWARE
ARG A:110 , SER A:111 , SER A:112 , ARG A:115 , MG A:2195 , HOH A:2222 , HOH A:2232 , ALA B:124 , ARG B:126 , ASP B:128 , TRP B:131 , ILE B:135 , VAL B:136 , TYR B:171 , ARG B:174 , ALA B:177 , LYS B:178 , TYR B:179 , GLN B:182 , HOH B:3198 , HOH B:3220 , HOH B:3221 , HOH B:3226
BINDING SITE FOR RESIDUE DCP B 2194
09
AC9
SOFTWARE
ARG B:110 , SER B:111 , SER B:112 , ARG B:115 , MG B:3195 , ALA C:124 , ARG C:126 , ASP C:128 , TRP C:131 , ILE C:135 , VAL C:136 , TYR C:171 , ARG C:174 , ALA C:177 , LYS C:178 , TYR C:179 , GLN C:182 , HOH C:3198 , HOH C:3204 , HOH C:3220
BINDING SITE FOR RESIDUE DCP C 3194
10
BC1
SOFTWARE
ALA D:124 , ARG D:126 , ASP D:128 , TRP D:131 , ILE D:135 , VAL D:136 , TYR D:171 , ARG D:174 , ALA D:177 , LYS D:178 , TYR D:179 , GLN D:182 , HOH D:5203 , HOH D:5208 , HOH D:5217 , HOH D:5227 , HOH D:5231 , ARG F:110 , SER F:111 , SER F:112 , ARG F:115 , MG F:4195 , HOH F:6228
BINDING SITE FOR RESIDUE DCP D 4194
11
BC2
SOFTWARE
ARG D:110 , SER D:111 , SER D:112 , ARG D:115 , MG D:5195 , HOH D:5233 , ALA E:124 , ARG E:126 , ASP E:128 , TRP E:131 , ILE E:135 , VAL E:136 , TYR E:171 , ARG E:174 , ALA E:177 , LYS E:178 , TYR E:179 , GLN E:182 , HOH E:6216 , HOH E:6228 , HOH E:6230 , HOH E:6245
BINDING SITE FOR RESIDUE DCP E 5194
12
BC3
SOFTWARE
ARG E:110 , SER E:111 , SER E:112 , ARG E:115 , MG E:6195 , ALA F:124 , ARG F:126 , ASP F:128 , TRP F:131 , ILE F:135 , VAL F:136 , TYR F:171 , ARG F:174 , ALA F:177 , LYS F:178 , TYR F:179 , GLN F:182 , HOH F:6195 , HOH F:6197 , HOH F:6211 , HOH F:6212 , HOH F:6218 , HOH F:6227
BINDING SITE FOR RESIDUE DCP F 6194
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1xs4a_ (A:)
1b: SCOP_d1xs4b_ (B:)
1c: SCOP_d1xs4c_ (C:)
1d: SCOP_d1xs4d_ (D:)
1e: SCOP_d1xs4e_ (E:)
1f: SCOP_d1xs4f_ (F:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-clip
(280)
Superfamily
:
dUTPase-like
(122)
Family
:
dUTPase-like
(71)
Protein domain
:
Deoxycytidine triphosphate deaminase (dCTP deaminase)
(9)
Escherichia coli [TaxId: 562]
(6)
1a
d1xs4a_
A:
1b
d1xs4b_
B:
1c
d1xs4c_
C:
1d
d1xs4d_
D:
1e
d1xs4e_
E:
1f
d1xs4f_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1xs4A00 (A:2-193)
1b: CATH_1xs4B00 (B:2-193)
1c: CATH_1xs4C00 (C:2-193)
1d: CATH_1xs4D00 (D:2-193)
1e: CATH_1xs4E00 (E:2-193)
1f: CATH_1xs4F00 (F:2-193)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
(52)
Homologous Superfamily
:
[code=2.70.40.10, no name defined]
(51)
Escherichia coli. Organism_taxid: 562.
(9)
1a
1xs4A00
A:2-193
1b
1xs4B00
B:2-193
1c
1xs4C00
C:2-193
1d
1xs4D00
D:2-193
1e
1xs4E00
E:2-193
1f
1xs4F00
F:2-193
[
close CATH info
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_dUTPase_1xs4F01 (F:72-189)
1b: PFAM_dUTPase_1xs4F02 (F:72-189)
1c: PFAM_dUTPase_1xs4F03 (F:72-189)
1d: PFAM_dUTPase_1xs4F04 (F:72-189)
1e: PFAM_dUTPase_1xs4F05 (F:72-189)
1f: PFAM_dUTPase_1xs4F06 (F:72-189)
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(
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)
Clan
:
dUTPase
(38)
Family
:
dUTPase
(38)
Escherichia coli (strain K12)
(8)
1a
dUTPase-1xs4F01
F:72-189
1b
dUTPase-1xs4F02
F:72-189
1c
dUTPase-1xs4F03
F:72-189
1d
dUTPase-1xs4F04
F:72-189
1e
dUTPase-1xs4F05
F:72-189
1f
dUTPase-1xs4F06
F:72-189
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