Structure of PDB 2gjw Chain D

Receptor sequence
>2gjwD (length=304) Species: 2234 (Archaeoglobus fulgidus) [Search protein sequence]
IGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELED
VLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKT
IRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAG
VLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNAD
REELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVES
VDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFE
RVKV
3D structure
PDB2gjw RNA Recognition and Cleavage by an Splicing Endonuclease
ChainD
Resolution2.85 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) Y249 H260 K290
Catalytic site (residue number reindexed from 1) Y245 H256 K286
Enzyme Commision number 4.6.1.16: tRNA-intron lyase.
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 D R283 N287 R289 R305 R279 N283 R285 R301
BS02 rna D Y249 L258 H260 S261 Y245 L254 H256 S257
BS03 rna D H260 K290 H256 K286
Gene Ontology
Molecular Function
GO:0000213 tRNA-intron endonuclease activity
GO:0003676 nucleic acid binding
GO:0016829 lyase activity
Biological Process
GO:0000379 tRNA-type intron splice site recognition and cleavage
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation
GO:0008033 tRNA processing

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2gjw, PDBe:2gjw, PDBj:2gjw
PDBsum2gjw
PubMed16690865
UniProtO29362|ENDA_ARCFU tRNA-splicing endonuclease (Gene Name=endA)

[Back to BioLiP]