5J5V

CdiA-CT from uropathogenic Escherichia coli in complex with cognate immunity protein and CysK

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d5j5vd_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	(Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)
A	d5j5va_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	(Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PALP	e5j5vD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
A	PALP	e5j5vA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
B	Ntox28	e5j5vB1	A: alpha arrays	X: CdiA C-terminal nuclease domain (From Topology)	H: CdiA C-terminal nuclease domain (From Topology)	T: CdiA C-terminal nuclease domain	F: Ntox28	ECOD (1.6)
E	Ntox28	e5j5vE1	A: alpha arrays	X: CdiA C-terminal nuclease domain (From Topology)	H: CdiA C-terminal nuclease domain (From Topology)	T: CdiA C-terminal nuclease domain	F: Ntox28	ECOD (1.6)
F	EUF08234	e5j5vF1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Immunity protein CdiI (From Topology)	T: Immunity protein CdiI	F: EUF08234	ECOD (1.6)
C	EUF08234	e5j5vC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Immunity protein CdiI (From Topology)	T: Immunity protein CdiI	F: EUF08234	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF00291	Pyridoxal-phosphate dependent enzyme (PALP)	Pyridoxal-phosphate dependent enzyme	-	Family
B, E	PF15605	Bacterial toxin 28 (Ntox28)	Bacterial toxin 28	-	Family
C, F	PF18616	CDI immunity proteins (CdiI_3)	CDI immunity proteins	Contact-dependent growth inhibition (CDI) is a widespread mechanism of bacterial competition. CDI+ bacteria deliver the toxic C-terminal region of contact-dependent inhibition A proteins (CdiA-CT) into neighboring target bacteria and produce CDI immu ...	Contact-dependent growth inhibition (CDI) is a widespread mechanism of bacterial competition. CDI+ bacteria deliver the toxic C-terminal region of contact-dependent inhibition A proteins (CdiA-CT) into neighboring target bacteria and produce CDI immunity proteins (CdiI) which bind CdiA-CT domains and neutralize their toxic activity to protect against self-inhibition. CdiI immunity proteins are also variable and only neutralize their cognate CdiA-CT toxins. Structure analysis of CdiI from Escherichia coli 536 (EC536) shows that is composed of a single domain and that it blocks the interaction with substrate, strongly suggesting that the immunity protein occludes the nuclease active site [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Cysteine synthase A	lyase activity catalytic activity cysteine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups	serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process cysteine biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process cysteine biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process organonitrogen compound metabolic process cysteine biosynthetic process from serine small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-serine metabolic process L-amino acid metabolic process cysteine metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process serine family amino acid biosynthetic process sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process	-
B, E	tRNA nuclease CdiA	toxin activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity RNA binding binding organic cyclic compound binding tRNA binding toxin activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity RNA binding binding organic cyclic compound binding tRNA binding nucleic acid binding tRNA-specific ribonuclease activity catalytic activity, acting on a tRNA	-	membrane cellular anatomical entity extracellular region other organism cell membrane other organism part host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region
C, F	Immunity protein CdiI	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR005856	Cysteine synthase	Family
A, D	IPR005859	Cysteine synthase CysK	Family
A, D	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily	Homologous Superfamily
A, D	IPR001926	Tryptophan synthase beta chain-like, PALP domain	Domain
A, D	IPR001216	Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site	Binding Site
B, E	IPR012334	Pectin lyase fold	Homologous Superfamily
B, E	IPR006914	VENN motif-containing domain	Domain
B, E	IPR028948	Bacterial toxin 28	Domain
B, E	IPR006626	Parallel beta-helix repeat	Repeat
B, E	IPR008638	Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain	Domain
B, E	IPR025157	Hemagglutinin repeat	Repeat
B, E	IPR010069	Toxin CdiA-like, Filamentous hemagglutinin motif repeats	Repeat
B, E	IPR011050	Pectin lyase fold/virulence factor	Homologous Superfamily
C, F	IPR040547	Immunity protein CdiI	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, D	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128
B, E	MSE	Parent Component: MET RESID: AA0119
C, F	MSE	Parent Component: MET RESID: AA0119

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.