3HI2 | pdb_00003hi2

Structure of the N-terminal domain of the E. coli antitoxin MqsA (YgiT/b3021) in complex with the E. coli toxin MqsR (YgiU/b3022)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Macro	e3hi2C1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Macro	ECOD (develop294)
A	Macro	e3hi2A1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Macro	ECOD (develop294)
D	Macro	e3hi2D1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Macro	ECOD (develop294)
B	HMA	e3hi2B1	A: alpha bundles	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: HMA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.10.20.860	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
A	3.10.20.860	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
D	3.30.2310.40	Alpha Beta	2-Layer Sandwich	YaeB-like fold		CATH (4.3.0)
B	3.30.2310.40	Alpha Beta	2-Layer Sandwich	YaeB-like fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF15731	Antitoxin component of bacterial toxin-antitoxin system, MqsA (MqsA_antitoxin)	Antitoxin component of bacterial toxin-antitoxin system, MqsA	MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin i ...	MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells [2] and it plays an essential role in biofilm regulation [3] and cell signalling [4]. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterised bacterial toxins [1].	Domain
B, D	PF15723	Motility quorum-sensing regulator, toxin of MqsA (MqsR_toxin)	Motility quorum-sensing regulator, toxin of MqsA	MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells [2] and it plays an essential role in biofilm regulation [3] and cell signalling [4]. It forms part of a b ...	MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells [2] and it plays an essential role in biofilm regulation [3] and cell signalling [4]. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterised bacterial toxins.y characterized bacterial toxins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	HTH-type transcriptional regulator mqsA(ygiT)	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity sequence-specific DNA binding DNA binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms	protein-containing complex transcription regulator complex toxin-antitoxin complex transcription repressor complex
B, D	Motility quorum-sensing regulator mqsR	RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism endonuclease activity hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process protein biosynthetic process post-transcriptional regulation of gene expression negative regulation of translation protein metabolic process negative regulation of protein metabolic process regulation of protein metabolic process translation negative regulation of gene expression regulation of translation catabolic process macromolecule catabolic process regulation of mRNA catabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of catabolic process mRNA metabolic process nucleobase-containing compound catabolic process regulation of mRNA stability regulation of RNA stability nucleic acid catabolic process regulation of mRNA metabolic process response to stimulus signaling quorum sensing cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus regulation of cell motility regulation of locomotion cell motility locomotion positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process positive regulation of biological process mRNA destabilization positive regulation of cellular process RNA destabilization positive regulation of catabolic process positive regulation of mRNA catabolic process cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms	protein-containing complex transcription regulator complex toxin-antitoxin complex transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR032758	Antitoxin MqsA/HigA-2	Family
A, C	IPR022453	Zinc finger, MqsA-type	Domain
A, C	IPR052359	Bacterial HTH-type regulators and antitoxins	Family
A, C	IPR001387	Cro/C1-type, helix-turn-helix domain	Domain
A, C	IPR022452	Antitoxin MqsA	Family
A, C	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily
B, D	IPR038493	Toxin MqsR superfamily	Homologous Superfamily
B, D	IPR031451	mRNA interferase toxin MqsR	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.