Structure of PDB 3lwp Chain A Binding Site BS02

Receptor Information

>3lwp Chain A (length=317) Species: 2261 (Pyrococcus furiosus)

RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGP
TSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAG
KEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRLRTRKVYYIEVLEIEGRD
VLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITL
HDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGA
DLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIA
VDVEKVFMPRDWYPKLW

Ligand information

>3lwp Chain E (length=13)

gagcgugcgguuu

.............

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3lwp Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): H63 H80 G82 T83 L107 Y113 G180 Y182 I183 R184
• Binding residue (residue number reindexed from 1): H53 H70 G72 T73 L97 Y103 G160 Y162 I163 R164

Enzymatic activity

• Catalytic site (original residue number in PDB): D85 Y113 R184
• Catalytic site (residue number reindexed from 1): D75 Y103 R164
• Enzyme Commision number: 5.4.99.25: tRNA pseudouridine(55) synthase.

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0009982 pseudouridine synthase activity
• GO:0016853 isomerase activity
• GO:0160148 tRNA pseudouridine(55) synthase activity

Biological Process

• GO:0000495 box H/ACA sno(s)RNA 3'-end processing
• GO:0001522 pseudouridine synthesis
• GO:0006396 RNA processing
• GO:0008033 tRNA processing
• GO:0009451 RNA modification
• GO:0031118 rRNA pseudouridine synthesis
• GO:0031119 tRNA pseudouridine synthesis
• GO:0031120 snRNA pseudouridine synthesis
• GO:1990481 mRNA pseudouridine synthesis

External links

• PDB: RCSB:3lwp, PDBe:3lwp, PDBj:3lwp
• PDBsum: 3lwp
• PubMed: 20615421
• UniProt: Q7LWY0|TRUB_PYRFU Probable tRNA pseudouridine synthase B (Gene Name=truB)