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6DJT
Structure of TYW1 with a lysine-pyruvate adduct bound
External Resource: Annotation
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation
Domain Annotation: ECOD Classification
ECOD Database Homepage
Chains
Family Name
Domain Identifier
Architecture
Possible Homology
Homology
Topology
Family
Provenance Source (Version)
A
PF04055,PF08608
e6djtA1
A: a/b barrels
X: TIM beta/alpha-barrel
H: TIM barrels (From Topology)
T: TIM barrels
F: PF04055,PF08608
ECOD (1.6)
Domain Annotation: CATH
CATH Database Homepage
Chain
Domain
Class
Architecture
Topology
Homology
Provenance Source (Version)
A
3.20.20.70
Alpha Beta
Alpha-Beta Barrel
TIM Barrel
Aldolase class I
CATH (4.3.0)
Protein Family Annotation
Pfam Database Homepage
Chains
Accession
Name
Description
Comments
Source
A
PF04055
Radical SAM superfamily (Radical_SAM)
Radical SAM superfamily
Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Domain
A
PF08608
Wyosine base formation (Wyosine_form)
Wyosine base formation
-
Family
Gene Ontology: Gene Product Annotation
Gene Ontology Database Homepage
Chains
Polymer
Molecular Function
Biological Process
Cellular Component
A
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase
iron-sulfur cluster binding
binding
4 iron, 4 sulfur cluster binding
metal cluster binding
small molecule binding
cation binding
ion binding
metal ion binding
oxo-acid-lyase activity
catalytic activity, acting on RNA
tRNA-4-demethylwyosine synthase activity
catalytic activity, acting on a nucleic acid
catalytic activity, acting on a tRNA
lyase activity
iron-sulfur cluster binding
binding
4 iron, 4 sulfur cluster binding
metal cluster binding
small molecule binding
cation binding
ion binding
metal ion binding
oxo-acid-lyase activity
catalytic activity, acting on RNA
tRNA-4-demethylwyosine synthase activity
catalytic activity, acting on a nucleic acid
catalytic activity, acting on a tRNA
lyase activity
catalytic activity
carbon-carbon lyase activity
Less
glycosyl compound metabolic process
wybutosine metabolic process
cellular biosynthetic process
organonitrogen compound biosynthetic process
carbohydrate derivative metabolic process
RNA metabolic process
nucleobase-containing compound metabolic process
RNA biosynthetic process
nucleic acid biosynthetic process
tRNA processing
RNA processing
carbohydrate derivative biosynthetic process
organonitrogen compound metabolic process
glycosyl compound biosynthetic process
glycosyl compound metabolic process
wybutosine metabolic process
cellular biosynthetic process
organonitrogen compound biosynthetic process
carbohydrate derivative metabolic process
RNA metabolic process
nucleobase-containing compound metabolic process
RNA biosynthetic process
nucleic acid biosynthetic process
tRNA processing
RNA processing
carbohydrate derivative biosynthetic process
organonitrogen compound metabolic process
glycosyl compound biosynthetic process
wybutosine biosynthetic process
cellular metabolic process
tRNA modification
primary metabolic process
gene expression
nucleobase-containing compound biosynthetic process
macromolecule biosynthetic process
nucleic acid metabolic process
tRNA metabolic process
RNA modification
biosynthetic process
macromolecule modification
metabolic process
cellular process
macromolecule metabolic process
Less
intracellular anatomical structure
cytoplasm
cellular anatomical entity
InterPro: Protein Family Classification
InterPro Database Homepage
Chains
Accession
Name
Type
A
IPR007197
Radical SAM
Domain
A
IPR013785
Aldolase-type TIM barrel
Homologous Superfamily
A
IPR013917
tRNA wybutosine-synthesis
Domain
A
IPR023993
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, archaea
Family
A
IPR034556
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase
Family
Protein Modification Annotation
Modified Residue(s)
Chain
Residue(s)
Description
A
KPI
Parent Component:
LYS
RESID
: 
AA0287
PSI-MOD
:  N6-pyruvic acid 2-iminyl-L-lysine
MOD:00292
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