2VMK | pdb_00002vmk

Crystal Structure of E. coli RNase E Apoprotein - Catalytic Domain

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MK0968-like	8102253	3002481	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DnaJ/Hsp40 cysteine-rich domain-like	8102255	3001550	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Type III KH-domain	8102257	3002727	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8039601	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8102249	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8102251	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8102251	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type III KH-domain	8102257	3002727	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8102249	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8102251	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DnaJ/Hsp40 cysteine-rich domain-like	8102255	3001550	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MK0968-like	8102253	3002481	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8039601	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8039601	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8102251	3000143	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8102249	3000100	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type III KH-domain	8102257	3002727	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MK0968-like	8102253	3002481	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8102251	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DnaJ/Hsp40 cysteine-rich domain-like	8102255	3001550	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleic acid-binding proteins	8039601	3000135	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8102251	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8102249	3000100	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MK0968-like	8102253	3002481	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type III KH-domain	8102257	3002727	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	RasGEF	e2vmkA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (v294.1)
B	Actin	e2vmkB16	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: Actin	ECOD (v294.1)
C	RasGEF	e2vmkC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (v294.1)
D	Glycolytic	e2vmkD1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F: Glycolytic	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1260.20	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
B	3.40.1260.20	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
C	3.40.1260.20	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
D	3.40.1260.20	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF20833	RNase E/G, Thioredoxin-like domain (RNase_E_G_Thio)	RNase E/G, Thioredoxin-like domain	Both RNase E and its homologue RNase G are endoribonucleases that play central roles in RNA processing. RNase E shows two globular domains. This entry represents the smaller domain, which shows a thioredoxin-like fold [1-3].	Domain
A, B, C, D	PF10150	Ribonuclease E/G family (RNase_E_G)	Ribonuclease E/G family	-	Family
A, B, C, D	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RIBONUCLEASE E	RNA binding binding rRNA binding nucleic acid binding tRNA binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding 7S RNA binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA binding binding rRNA binding nucleic acid binding tRNA binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding 7S RNA binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity ribonuclease E activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity protein binding enzyme binding DEAD/H-box RNA helicase binding molecular adaptor activity transition metal ion binding zinc ion binding identical protein binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein homotetramerization protein tetramerization protein homooligomerization ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein homotetramerization protein tetramerization protein homooligomerization ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process RNA processing rRNA metabolic process tRNA metabolic process tRNA processing catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process mRNA metabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process rRNA 5'-end processing RNA 5'-end processing	cellular anatomical structure membrane bacterial degradosome exosome (RNase complex) protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cytosol cytoplasmic exosome (RNase complex) exoribonuclease complex endoribonuclease complex intracellular protein-containing complex endonuclease complex cellular anatomical structure membrane bacterial degradosome exosome (RNase complex) protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cytosol cytoplasmic exosome (RNase complex) exoribonuclease complex endoribonuclease complex intracellular protein-containing complex endonuclease complex cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR028878	Ribonuclease E	Family
A, B, C, D	IPR004659	Ribonuclease E/G	Family
A, B, C, D	IPR019307	RNA-binding protein AU-1/Ribonuclease E/G	Domain
A, B, C, D	IPR003029	S1 domain	Domain
A, B, C, D	IPR021968	Polyribonucleotide phosphorylase C-terminal	Domain
A, B, C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C, D	IPR048583	RNase E/G, thioredoxin-like domain	Domain