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1OBH
Asym. Unit
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Asym.Unit (140 KB)
Biol.Unit 1 (134 KB)
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(1)
Title
:
LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A PRE-TRANSFER EDITING SUBSTRATE ANALOGUE IN BOTH SYNTHETIC ACTIVE SITE AND EDITING SITE
Authors
:
S. Cusack, A. Yaremchuk, M. Tukalo
Date
:
31 Jan 03 (Deposition) - 09 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Synthetase, Aminoacyl-Trna Synthetase, Class I Aminoacyl-Trna Synthetase, Atp + L-Leucine + Trna (Leu) -> Amp + Ppi L- Leucyl-Trna(Leu)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Lincecum, M. Tukalo, A. Yaremchuk, R. Mursinna, A. Williams, B. Sproat, W. Van Den Eynde, A. Link, S. Van Calenbergh, M. Grotli, S. Martinis, S. Cusack
Structural And Mechanistic Basis Of Pre- And Posttransfer Editing By Leucyl-Trna Synthetase
Mol. Cell V. 11 951 2003
(for further references see the
PDB file header
)
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: MERCURY (II) ION (HGa)
2a: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN... (LMSa)
2b: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN... (LMSb)
3a: NORVALINE (NVAa)
3b: NORVALINE (NVAb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
View:
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Label:
No.
Name
Count
Type
Full Name
1
HG
1
Ligand/Ion
MERCURY (II) ION
2
LMS
2
Ligand/Ion
[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYLSULFAMATE
3
NVA
2
Ligand/Ion
NORVALINE
4
SO4
6
Ligand/Ion
SULFATE ION
[
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:714 , GLU A:715 , GLY A:716 , ARG A:719 , LYS A:760
BINDING SITE FOR RESIDUE SO4 A1501
02
AC2
SOFTWARE
GLY A:707 , ARG A:769 , ARG A:773 , TRP A:795
BINDING SITE FOR RESIDUE SO4 A1502
03
AC3
SOFTWARE
VAL A:564 , GLU A:565 , GLU A:566 , HOH A:2193 , HOH A:2194
BINDING SITE FOR RESIDUE SO4 A1503
04
AC4
SOFTWARE
ARG A:759 , HOH A:2178
BINDING SITE FOR RESIDUE SO4 A1504
05
AC5
SOFTWARE
ARG A:426 , ARG A:428 , ASP A:499
BINDING SITE FOR RESIDUE SO4 A1505
06
AC6
SOFTWARE
HIS A:49 , HIS A:52 , SER A:639 , LYS A:640 , HOH A:2134
BINDING SITE FOR RESIDUE SO4 A1506
07
AC7
SOFTWARE
TYR A:102 , CYS A:128 , GLU A:129
BINDING SITE FOR RESIDUE HG A1815
08
AC8
SOFTWARE
PHE A:41 , TYR A:43 , ASP A:80 , TYR A:535 , HIS A:545 , LMS A:1817
BINDING SITE FOR RESIDUE NVA A1816
09
AC9
SOFTWARE
PRO A:42 , TYR A:43 , GLY A:51 , HIS A:52 , ASN A:55 , TYR A:56 , MET A:576 , VAL A:577 , MET A:638 , NVA A:1816 , HOH A:2196
BINDING SITE FOR RESIDUE LMS A1817
10
BC1
SOFTWARE
THR A:247 , THR A:252 , MET A:338 , VAL A:340 , ASP A:347 , LMS A:1819 , HOH A:2077
BINDING SITE FOR RESIDUE NVA A1818
11
BC2
SOFTWARE
THR A:247 , THR A:248 , ARG A:249 , TYR A:327 , VAL A:328 , LEU A:329 , TYR A:332 , ILE A:337 , ASP A:344 , NVA A:1818 , HOH A:2197
BINDING SITE FOR RESIDUE LMS A1819
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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
All PROSITE Patterns/Profiles
;
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Sorry, no Info available
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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, 3)
Info
All SCOP Domains
1a: SCOP_d1obha1 (A:687-814)
2a: SCOP_d1obha2 (A:226-417)
3a: SCOP_d1obha3 (A:1-225,A:418-686)
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Classes
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
(48)
Superfamily
:
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
(48)
Family
:
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
(30)
Protein domain
:
Leucyl-tRNA synthetase (LeuRS)
(3)
Thermus thermophilus [TaxId: 274]
(3)
1a
d1obha1
A:687-814
Class
:
All beta proteins
(24004)
Fold
:
ValRS/IleRS/LeuRS editing domain
(19)
Superfamily
:
ValRS/IleRS/LeuRS editing domain
(19)
Family
:
ValRS/IleRS/LeuRS editing domain
(19)
Protein domain
:
Leucyl-tRNA synthetase (LeuRS)
(3)
Thermus thermophilus [TaxId: 274]
(3)
2a
d1obha2
A:226-417
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
Nucleotidylyl transferase
(325)
Family
:
Class I aminoacyl-tRNA synthetases (RS), catalytic domain
(137)
Protein domain
:
Leucyl-tRNA synthetase (LeuRS)
(3)
Thermus thermophilus [TaxId: 274]
(3)
3a
d1obha3
A:1-225,A:418-686
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CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_1obhA01 (A:31-222,A:419-576,A:639-646)
2a: CATH_1obhA02 (A:227-418)
3a: CATH_1obhA04 (A:655-814)
4a: CATH_1obhA03 (A:577-638)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(3)
1a
1obhA01
A:31-222,A:419-576,A:639-646
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Isoleucyl-tRNA Synthetase; domain 2
(21)
Homologous Superfamily
:
Isoleucyl-tRNA Synthetase; Domain 2
(21)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(2)
2a
1obhA02
A:227-418
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Isoleucyl-tRNA Synthetase; Domain 1
(35)
Homologous Superfamily
:
Isoleucyl-tRNA Synthetase; Domain 1
(35)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(2)
3a
1obhA04
A:655-814
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Leucyl-tRNA synthetase, domain 3
(3)
Homologous Superfamily
:
Leucyl-tRNA synthetase, domain 3
(3)
Thermus thermophilus. Organism_taxid: 262724. Strain: hb27.
(2)
4a
1obhA03
A:577-638
[
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Pfam Domains
(4, 4)
Info
all PFAM domains
1a: PFAM_tRNA_synt_1_1obhA01 (A:413-581)
2a: PFAM_tRNA_synt_1_2_1obhA02 (A:221-406)
3a: PFAM_tRNA_synt_1g_1obhA03 (A:35-229)
4a: PFAM_Anticodon_1_1obhA04 (A:718-814)
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Clans
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(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
HUP
(230)
Family
:
tRNA-synt_1
(17)
Thermus thermophilus
(5)
1a
tRNA-synt_1-1obhA01
A:413-581
Family
:
tRNA-synt_1_2
(5)
Thermus thermophilus
(3)
2a
tRNA-synt_1_2-1obhA02
A:221-406
Family
:
tRNA-synt_1g
(19)
Thermus thermophilus
(3)
3a
tRNA-synt_1g-1obhA03
A:35-229
Clan
:
no clan defined [family: Anticodon_1]
(10)
Family
:
Anticodon_1
(10)
Thermus thermophilus
(3)
4a
Anticodon_1-1obhA04
A:718-814
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