8ZYC | pdb_00008zyc

Cryo-EM structure of uropathogenic Escherichia coli CysK:CdiA:tRNA complex A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth E]	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8098394	3001427	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8098394	3001427	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth E]	PF00291	Pyridoxal-phosphate dependent enzyme (PALP)	Pyridoxal-phosphate dependent enzyme	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	tRNAIleGAU	-	-	-
B	tRNA nuclease CdiA	toxin activity endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity RNA binding binding tRNA binding nucleic acid binding tRNA-specific ribonuclease activity catalytic activity, acting on a tRNA	-	cellular anatomical structure membrane extracellular region other organism cell membrane other organism part host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region
A, D [auth E]	Cysteine synthase A	carbon-halide lyase activity S-carboxymethylcysteine synthase activity lyase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cysteine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups vitamin binding vitamin B6 binding carbon-halide lyase activity S-carboxymethylcysteine synthase activity lyase activity catalytic activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cysteine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding carbon-sulfur lyase activity L-cysteine desulfhydrase activity	amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process serine family amino acid metabolic process oxoacid metabolic process sulfur amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process cysteine biosynthetic process amino acid biosynthetic process biosynthetic process amino acid metabolic process primary metabolic process metabolic process cellular process serine family amino acid metabolic process oxoacid metabolic process sulfur amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process cysteine biosynthetic process small molecule metabolic process sulfur compound metabolic process cysteine biosynthetic process from serine small molecule biosynthetic process carboxylic acid metabolic process L-serine metabolic process L-amino acid metabolic process cysteine metabolic process proteinogenic amino acid metabolic process sulfur compound biosynthetic process serine family amino acid biosynthetic process sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex transferase complex cytoplasm cysteine synthase complex cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR012334	Pectin lyase fold	Homologous Superfamily
B	IPR006914	VENN motif-containing domain	Domain
B	IPR006626	Parallel beta-helix repeat	Repeat
B	IPR008638	Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain	Domain
B	IPR025157	Hemagglutinin repeat	Repeat
B	IPR010069	Toxin CdiA-like, Filamentous hemagglutinin motif repeats	Repeat
B	IPR011050	Pectin lyase fold/virulence factor	Homologous Superfamily
A, D [auth E]	IPR005856	Cysteine synthase	Family
A, D [auth E]	IPR005859	Cysteine synthase CysK	Family
A, D [auth E]	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily	Homologous Superfamily
A, D [auth E]	IPR001216	Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site	Binding Site
A, D [auth E]	IPR050214	Cysteine synthase/Cystathionine beta-synthase	Family
A, D [auth E]	IPR001926	Tryptophan synthase beta chain-like, PALP domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	T6A	Parent Component: A
A, D [auth E]	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.