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1KOG
Asym. Unit
Info
Asym.Unit (680 KB)
Biol.Unit 1 (175 KB)
Biol.Unit 2 (174 KB)
Biol.Unit 3 (173 KB)
Biol.Unit 4 (174 KB)
Biol.Unit 5 (175 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE INTERACTING WITH THE ESSENTIAL DOMAIN OF ITS MRNA OPERATOR
Authors
:
A. Torres-Larrios, A. C. Dock-Bregeon, P. Romby, B. Rees, R. Sankaranarayanan, J. Caillet, M. Springer, C. Ehresmann, B. Ehresmann, D. Moras
Date
:
20 Dec 01 (Deposition) - 26 Apr 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,I,J (1x)
Biol. Unit 2: C,D,K,L (1x)
Biol. Unit 3: E,F,M,N (1x)
Biol. Unit 4: G,O (2x)
Biol. Unit 5: H,P (2x)
Keywords
:
Protein-Rna Complex, Rna Stem-Loop, Rna Double Helix, Rna Base Triples, Ligase/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Torres-Larios, A. C. Dock-Bregeon, P. Romby, B. Rees, R. Sankaranarayanan, J. Caillet, M. Springer, C. Ehresmann, B. Ehresmann, D. Moras
Structural Basis Of Translational Control By Escherichia Coli Threonyl Trna Synthetase.
Nat. Struct. Biol. V. 9 343 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 16)
Info
All Hetero Components
1a: 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADE... (TSBa)
1b: 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADE... (TSBb)
1c: 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADE... (TSBc)
1d: 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADE... (TSBd)
1e: 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADE... (TSBe)
1f: 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADE... (TSBf)
1g: 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADE... (TSBg)
1h: 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADE... (TSBh)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
TSB
8
Ligand/Ion
5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE
2
ZN
8
Ligand/Ion
ZINC ION
[
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]
Sites
(16, 16)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:334 , HIS A:385 , TYR A:462 , HIS A:511 , TSB A:2002
BINDING SITE FOR RESIDUE ZN A 1
02
AC2
SOFTWARE
CYS B:334 , HIS B:385 , HIS B:511 , TSB B:3002
BINDING SITE FOR RESIDUE ZN B 1
03
AC3
SOFTWARE
CYS C:334 , HIS C:385 , TYR C:462 , HIS C:511 , TSB C:4002
BINDING SITE FOR RESIDUE ZN C 1
04
AC4
SOFTWARE
CYS D:334 , HIS D:385 , HIS D:511 , TSB D:5002
BINDING SITE FOR RESIDUE ZN D 1
05
AC5
SOFTWARE
CYS E:334 , HIS E:385 , HIS E:511 , TSB E:6002
BINDING SITE FOR RESIDUE ZN E 1
06
AC6
SOFTWARE
CYS F:334 , HIS F:385 , TYR F:462 , HIS F:511 , TSB F:7002
BINDING SITE FOR RESIDUE ZN F 1
07
AC7
SOFTWARE
CYS G:334 , HIS G:385 , TYR G:462 , HIS G:511 , TSB G:8002
BINDING SITE FOR RESIDUE ZN G 1
08
AC8
SOFTWARE
CYS H:334 , HIS H:385 , TYR H:462 , HIS H:511 , TSB H:9002
BINDING SITE FOR RESIDUE ZN H 1
09
AC9
SOFTWARE
ZN A:1 , MET A:332 , CYS A:334 , ARG A:363 , GLU A:365 , MET A:374 , VAL A:376 , PHE A:379 , GLN A:381 , ASP A:383 , ALA A:384 , HIS A:385 , TYR A:462 , GLN A:479 , CYS A:480 , THR A:482 , GLN A:484 , HIS A:511 , ARG A:512 , GLY A:516 , SER A:517 , ARG A:520
BINDING SITE FOR RESIDUE TSB A 2002
10
BC1
SOFTWARE
ZN B:1 , MET B:332 , CYS B:334 , ARG B:363 , GLU B:365 , MET B:374 , VAL B:376 , PHE B:379 , GLN B:381 , ASP B:383 , ALA B:384 , HIS B:385 , TYR B:462 , GLN B:479 , CYS B:480 , THR B:482 , GLN B:484 , HIS B:511 , ARG B:512 , GLY B:516 , SER B:517 , ARG B:520
BINDING SITE FOR RESIDUE TSB B 3002
11
BC2
SOFTWARE
ZN C:1 , MET C:332 , CYS C:334 , ARG C:363 , GLU C:365 , MET C:374 , VAL C:376 , PHE C:379 , GLN C:381 , ASP C:383 , ALA C:384 , HIS C:385 , TYR C:462 , GLN C:479 , CYS C:480 , GLN C:484 , HIS C:511 , ARG C:512 , GLY C:516 , SER C:517 , ARG C:520
BINDING SITE FOR RESIDUE TSB C 4002
12
BC3
SOFTWARE
ZN D:1 , MET D:332 , CYS D:334 , ARG D:363 , GLU D:365 , MET D:374 , VAL D:376 , PHE D:379 , GLN D:381 , ASP D:383 , ALA D:384 , HIS D:385 , TYR D:462 , GLN D:479 , CYS D:480 , THR D:482 , GLN D:484 , HIS D:511 , ARG D:512 , GLY D:516 , SER D:517 , ARG D:520
BINDING SITE FOR RESIDUE TSB D 5002
13
BC4
SOFTWARE
ZN E:1 , MET E:332 , CYS E:334 , ARG E:363 , GLU E:365 , MET E:374 , VAL E:376 , PHE E:379 , GLN E:381 , ASP E:383 , ALA E:384 , HIS E:385 , TYR E:462 , GLN E:479 , CYS E:480 , THR E:482 , GLN E:484 , HIS E:511 , ARG E:512 , ALA E:513 , GLY E:516 , SER E:517 , ARG E:520
BINDING SITE FOR RESIDUE TSB E 6002
14
BC5
SOFTWARE
ZN F:1 , MET F:332 , CYS F:334 , ARG F:363 , GLU F:365 , MET F:374 , VAL F:376 , PHE F:379 , GLN F:381 , ASP F:383 , ALA F:384 , HIS F:385 , TYR F:462 , GLN F:479 , CYS F:480 , THR F:482 , GLN F:484 , HIS F:511 , ARG F:512 , GLY F:516 , SER F:517 , ARG F:520
BINDING SITE FOR RESIDUE TSB F 7002
15
BC6
SOFTWARE
ZN G:1 , MET G:332 , CYS G:334 , ARG G:363 , GLU G:365 , MET G:374 , VAL G:376 , PHE G:379 , GLN G:381 , ASP G:383 , ALA G:384 , HIS G:385 , TYR G:462 , GLN G:479 , CYS G:480 , THR G:482 , GLN G:484 , HIS G:511 , ARG G:512 , GLY G:516 , SER G:517 , ARG G:520
BINDING SITE FOR RESIDUE TSB G 8002
16
BC7
SOFTWARE
ZN H:1 , MET H:332 , CYS H:334 , ARG H:363 , GLU H:365 , MET H:374 , VAL H:376 , PHE H:379 , GLN H:381 , ASP H:383 , ALA H:384 , HIS H:385 , TYR H:462 , GLN H:479 , CYS H:480 , THR H:482 , GLN H:484 , HIS H:511 , ARG H:512 , GLY H:516 , SER H:517 , ARG H:520
BINDING SITE FOR RESIDUE TSB H 9002
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1koga2 (A:242-532)
1b: SCOP_d1kogb2 (B:242-532)
1c: SCOP_d1kogc2 (C:242-532)
1d: SCOP_d1kogd2 (D:242-532)
1e: SCOP_d1koge2 (E:242-532)
1f: SCOP_d1kogf2 (F:242-532)
1g: SCOP_d1kogg2 (G:242-532)
1h: SCOP_d1kogh2 (H:242-532)
2a: SCOP_d1koga1 (A:533-642)
2b: SCOP_d1kogb1 (B:533-642)
2c: SCOP_d1kogc1 (C:533-642)
2d: SCOP_d1kogd1 (D:533-642)
2e: SCOP_d1koge1 (E:533-642)
2f: SCOP_d1kogf1 (F:533-642)
2g: SCOP_d1kogg1 (G:533-642)
2h: SCOP_d1kogh1 (H:533-642)
View:
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Classes
(
)
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)
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(
)
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(
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(
)
Families
(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Class II aaRS and biotin synthetases
(165)
Superfamily
:
Class II aaRS and biotin synthetases
(165)
Family
:
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
(103)
Protein domain
:
Threonyl-tRNA synthetase (ThrRS)
(7)
Escherichia coli [TaxId: 562]
(5)
1a
d1koga2
A:242-532
1b
d1kogb2
B:242-532
1c
d1kogc2
C:242-532
1d
d1kogd2
D:242-532
1e
d1koge2
E:242-532
1f
d1kogf2
F:242-532
1g
d1kogg2
G:242-532
1h
d1kogh2
H:242-532
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Anticodon-binding domain-like
(97)
Superfamily
:
Class II aaRS ABD-related
(40)
Family
:
Anticodon-binding domain of Class II aaRS
(33)
Protein domain
:
Threonyl-tRNA synthetase (ThrRS), C-terminal domain
(7)
Escherichia coli [TaxId: 562]
(5)
2a
d1koga1
A:533-642
2b
d1kogb1
B:533-642
2c
d1kogc1
C:533-642
2d
d1kogd1
D:533-642
2e
d1koge1
E:533-642
2f
d1kogf1
F:533-642
2g
d1kogg1
G:533-642
2h
d1kogh1
H:533-642
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1kogA01 (A:242-530)
1b: CATH_1kogB01 (B:242-530)
1c: CATH_1kogC01 (C:242-530)
1d: CATH_1kogD01 (D:242-530)
1e: CATH_1kogE01 (E:242-530)
1f: CATH_1kogF01 (F:242-530)
1g: CATH_1kogG01 (G:242-530)
1h: CATH_1kogH01 (H:242-530)
2a: CATH_1kogA02 (A:531-642)
2b: CATH_1kogB02 (B:531-642)
2c: CATH_1kogC02 (C:531-642)
2d: CATH_1kogD02 (D:531-642)
2e: CATH_1kogE02 (E:531-642)
2f: CATH_1kogF02 (F:531-642)
2g: CATH_1kogG02 (G:531-642)
2h: CATH_1kogH02 (H:531-642)
View:
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
BirA Bifunctional Protein; domain 2
(111)
Homologous Superfamily
:
Bira Bifunctional Protein; Domain 2
(111)
[unclassified]
(3)
1a
1kogA01
A:242-530
1b
1kogB01
B:242-530
1c
1kogC01
C:242-530
1d
1kogD01
D:242-530
1e
1kogE01
E:242-530
1f
1kogF01
F:242-530
1g
1kogG01
G:242-530
1h
1kogH01
H:242-530
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.800, no name defined]
(40)
[unclassified]
(1)
2a
1kogA02
A:531-642
2b
1kogB02
B:531-642
2c
1kogC02
C:531-642
2d
1kogD02
D:531-642
2e
1kogE02
E:531-642
2f
1kogF02
F:531-642
2g
1kogG02
G:531-642
2h
1kogH02
H:531-642
[
close CATH info
]
Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_HGTP_anticodon_1kogH01 (H:541-631)
1b: PFAM_HGTP_anticodon_1kogH02 (H:541-631)
1c: PFAM_HGTP_anticodon_1kogH03 (H:541-631)
1d: PFAM_HGTP_anticodon_1kogH04 (H:541-631)
1e: PFAM_HGTP_anticodon_1kogH05 (H:541-631)
1f: PFAM_HGTP_anticodon_1kogH06 (H:541-631)
1g: PFAM_HGTP_anticodon_1kogH07 (H:541-631)
1h: PFAM_HGTP_anticodon_1kogH08 (H:541-631)
2a: PFAM_tRNA_synt_2b_1kogH09 (H:273-440)
2b: PFAM_tRNA_synt_2b_1kogH10 (H:273-440)
2c: PFAM_tRNA_synt_2b_1kogH11 (H:273-440)
2d: PFAM_tRNA_synt_2b_1kogH12 (H:273-440)
2e: PFAM_tRNA_synt_2b_1kogH13 (H:273-440)
2f: PFAM_tRNA_synt_2b_1kogH14 (H:273-440)
2g: PFAM_tRNA_synt_2b_1kogH15 (H:273-440)
2h: PFAM_tRNA_synt_2b_1kogH16 (H:273-440)
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Organisms
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(
)
Clan
:
IIaaRS-ABD
(13)
Family
:
HGTP_anticodon
(13)
Escherichia coli (strain K12)
(4)
1a
HGTP_anticodon-1kogH01
H:541-631
1b
HGTP_anticodon-1kogH02
H:541-631
1c
HGTP_anticodon-1kogH03
H:541-631
1d
HGTP_anticodon-1kogH04
H:541-631
1e
HGTP_anticodon-1kogH05
H:541-631
1f
HGTP_anticodon-1kogH06
H:541-631
1g
HGTP_anticodon-1kogH07
H:541-631
1h
HGTP_anticodon-1kogH08
H:541-631
Clan
:
tRNA_synt_II
(64)
Family
:
tRNA-synt_2b
(25)
Escherichia coli (strain K12)
(4)
2a
tRNA-synt_2b-1kogH09
H:273-440
2b
tRNA-synt_2b-1kogH10
H:273-440
2c
tRNA-synt_2b-1kogH11
H:273-440
2d
tRNA-synt_2b-1kogH12
H:273-440
2e
tRNA-synt_2b-1kogH13
H:273-440
2f
tRNA-synt_2b-1kogH14
H:273-440
2g
tRNA-synt_2b-1kogH15
H:273-440
2h
tRNA-synt_2b-1kogH16
H:273-440
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