Annotations: 3VU3

Crystal structure of the Hfq and catalase HPII complex

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3vu3a2	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Catalase, C-terminal domain	Catalase, C-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3vu3a1	Multi-domain proteins (alpha and beta)	Heme-dependent catalase-like	Heme-dependent catalase-like	Heme-dependent catalases	Catalase II	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B [auth C]	d3vu3c_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C [auth D]	d3vu3d_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D [auth E]	d3vu3e_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E [auth F]	d3vu3f_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F [auth G]	d3vu3g_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G [auth H]	d3vu3h_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Heme-dependent catalase-like	8038396	3001681	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8038393	3001405	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	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)
A	Tubulin	e3vu3A4	A: alpha arrays	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Tubulin	ECOD (v295)
B [auth C]	Fz	e3vu3C1	A: alpha arrays	X: Suppressor of Fused, C-terminal domain	H: HTH	T: winged helix domain	F: Fz	ECOD (v295)
C [auth D]	Fz	e3vu3D1	A: alpha arrays	X: Suppressor of Fused, C-terminal domain	H: HTH	T: winged helix domain	F: Fz	ECOD (v295)
D [auth E]	Fz	e3vu3E1	A: alpha arrays	X: Suppressor of Fused, C-terminal domain	H: HTH	T: winged helix domain	F: Fz	ECOD (v295)
E [auth F]	Fz	e3vu3F1	A: alpha arrays	X: Suppressor of Fused, C-terminal domain	H: HTH	T: winged helix domain	F: Fz	ECOD (v295)
F [auth G]	Fz	e3vu3G1	A: alpha arrays	X: Suppressor of Fused, C-terminal domain	H: HTH	T: winged helix domain	F: Fz	ECOD (v295)
G [auth H]	Fz	e3vu3H1	A: alpha arrays	X: Suppressor of Fused, C-terminal domain	H: HTH	T: winged helix domain	F: Fz	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.180.10	Mainly Beta	Beta Barrel	Catalase HpII, Chain A, domain 1	Catalase core domain	CATH (4.3.0)
A	1.20.1370.20	Mainly Alpha	Up-down Bundle	Hemocyanin, N-terminal domain	Catalase, four-helical domain	CATH (4.3.0)
A	3.40.50.880	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Class I glutamine amidotransferase (GATase) domain	CATH (4.3.0)
B [auth C]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C [auth D]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D [auth E]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E [auth F]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
F [auth G]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G [auth H]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18011	C-terminal domain found in long catalases (Catalase_C)	C-terminal domain found in long catalases	This domain is found at the C-terminus of a variety of large catalase enzymes from bacteria. Structurally it is related to class I glutamine amidotransferase domains. The precise molecular function of this domain is uncertain.	Domain
A	PF06628	Catalase-related immune-responsive (Catalase-rel)	Catalase-related immune-responsive	-	Family
A	PF00199	Catalase (Catalase)	Catalase		Domain
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H]	PF17209	Hfq protein (Hfq)	Hfq protein	This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria [1]. It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA [2]. It ap ...	This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria [1]. It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA [2]. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage [3]. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam:RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor [4]. The name Hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Catalase HPII	peroxidase activity oxidoreductase activity antioxidant activity catalase activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding peroxidase activity oxidoreductase activity antioxidant activity catalase activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding identical protein binding protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process hydrogen peroxide catabolic process response to oxidative stress response to osmotic stress hyperosmotic response cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process hydrogen peroxide catabolic process response to oxidative stress response to osmotic stress hyperosmotic response response to abiotic stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H]	Protein hfq	DNA binding bent DNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding DNA binding bent DNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding RNA binding tRNA binding RNA folding chaperone	regulation of cellular process catabolic process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of biological quality regulation of nucleobase-containing compound metabolic process RNA catabolic process regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular process catabolic process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of biological quality regulation of nucleobase-containing compound metabolic process RNA catabolic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression biosynthetic process regulation of RNA stability nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of translation, ncRNA-mediated positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process translation positive regulation of translation, ncRNA-mediated positive regulation of gene expression regulation of translation tRNA metabolic process tRNA processing RNA processing negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process sRNA-mediated post-transcriptional gene silencing negative regulation of metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing	intracellular organelle bacterial nucleoid cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle nucleoid cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
A	IPR024708	Catalase active site	Active Site
A	IPR041399	Large catalase, C-terminal domain	Domain
A	IPR010582	Catalase immune-responsive domain	Domain
A	IPR043156	Catalase, mono-functional, haem-containing, clade 2, helical domain	Homologous Superfamily
A	IPR002226	Catalase haem-binding site	Binding Site
A	IPR020835	Catalase superfamily	Homologous Superfamily
A	IPR024712	Catalase, mono-functional, haem-containing, clade 2	Family
A	IPR011614	Catalase core domain	Domain
A	IPR018028	Catalase, mono-functional, haem-containing	Family
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H]	IPR005001	RNA-binding protein Hfq	Family
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H]	IPR047575	Sm domain	Domain
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], G [auth H]	IPR010920	LSM domain superfamily	Homologous Superfamily

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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.