1XM5 | pdb_00001xm5

Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054

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	d1xm5a_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Predicted metal-dependent hydrolase	Hypothetical protein YbeY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1xm5b_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Predicted metal-dependent hydrolase	Hypothetical protein YbeY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1xm5c_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Predicted metal-dependent hydrolase	Hypothetical protein YbeY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1xm5d_	Alpha and beta proteins (a+b)	Zincin-like	Metalloproteases ('zincins'), catalytic domain	Predicted metal-dependent hydrolase	Hypothetical protein YbeY	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Predicted metal-dependent hydrolase	8031621	4001500	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metalloproteases (zincins), catalytic domain	8043999	3001975	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8043999	3001975	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8043999	3001975	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8043999	3001975	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	UPF0054	e1xm5A1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: UPF0054	ECOD (1.6)
B	UPF0054	e1xm5B1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: UPF0054	ECOD (1.6)
C	UPF0054	e1xm5C1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: UPF0054	ECOD (1.6)
D	UPF0054	e1xm5D1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: UPF0054	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.390.30	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Metalloproteases ("zincins"), catalytic domain	CATH (4.3.0)
B	3.40.390.30	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Metalloproteases ("zincins"), catalytic domain	CATH (4.3.0)
C	3.40.390.30	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Metalloproteases ("zincins"), catalytic domain	CATH (4.3.0)
D	3.40.390.30	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Metalloproteases ("zincins"), catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02130	Endoribonuclease YbeY (YbeY)	Endoribonuclease YbeY	YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not proper ...	YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs [2,3,4]. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Hypothetical UPF0054 protein ybeY	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding 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 cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding 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 peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity metallopeptidase activity endopeptidase activity zinc ion binding	negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis ribosomal small subunit biogenesis rRNA processing RNA processing rRNA metabolic process response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus maturation of SSU-rRNA protein metabolic process translation protein biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR023091	Metalloprotease catalytic domain superfamily, predicted	Homologous Superfamily
A, B, C, D	IPR002036	Endoribonuclease YbeY	Family
A, B, C, D	IPR020549	Endoribonuclease YbeY, conserved site	Conserved Site

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.