Structure of PDB 3dh3 Chain C Binding Site BS01

Receptor Information
>3dh3 Chain C (length=239) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVK
VNGQLIEPREAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPI
GRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGM
SAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKL
ERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSE
Ligand information
>3dh3 Chain G (length=22) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaacgucgugagacaguucgg
.....<<<....>>>.......
Receptor-Ligand Complex Structure
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PDB3dh3 Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		R8 N10 K11 S20 R21 R22 D25 I42 G43 T82 E83 R99 F101 R105 D107 K108 S110 G120 V123 N124 L127 R128 K135 Y137 G184 L185 N186 R187 Q188 I189 R190 L203 S240
Binding residue
(residue number reindexed from 1)		R5 N7 K8 S17 R18 R19 D22 I39 G40 T79 E80 R96 F98 R102 D104 K105 S107 G117 V120 N121 L124 R125 K132 Y134 G181 L182 N183 R184 Q185 I186 R187 L200 S237
Enzymatic activity
Enzyme Commision number 5.4.99.-
5.4.99.21: 23S rRNA pseudouridine(2604) synthase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0009982 pseudouridine synthase activity
GO:0016853 isomerase activity
GO:0016866 intramolecular transferase activity
GO:0106029 tRNA pseudouridine synthase activity
GO:0120159 rRNA pseudouridine synthase activity
GO:0160138 23S rRNA pseudouridine(2604) synthase activity
Biological Process
GO:0000455 enzyme-directed rRNA pseudouridine synthesis
GO:0001522 pseudouridine synthesis
GO:0006364 rRNA processing
GO:0008033 tRNA processing
GO:0009451 RNA modification
GO:0031119 tRNA pseudouridine synthesis

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dh3, PDBe:3dh3, PDBj:3dh3
PDBsum3dh3
PubMed19298824
UniProtP32684|RLUF_ECOLI Dual-specificity RNA pseudouridine synthase RluF (Gene Name=rluF)

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