Structure of PDB 3dh3 Chain C

Receptor sequence

>3dh3C (length=239) Species: 562 (Escherichia coli)

DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVK
VNGQLIEPREAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPI
GRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGM
SAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKL
ERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSE

3D structure

• PDB: 3dh3 Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
• Chain: C
• Resolution: 3.0 Å

Enzymatic activity

• Enzyme Commision number: 5.4.99.-
  5.4.99.21: 23S rRNA pseudouridine(2604) synthase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	C	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	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

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

External links

• PDB: RCSB:3dh3, PDBe:3dh3, PDBj:3dh3
• PDBsum: 3dh3
• PubMed: 19298824
• UniProt: P32684|RLUF_ECOLI Dual-specificity RNA pseudouridine synthase RluF (Gene Name=rluF)