2FYM | pdb_00002fym

Crystal structure of E. coli enolase complexed with the minimal binding segment of RNase E.

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)
F	d2fymf1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	Enolase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2fymf2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2fymd1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	Enolase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2fymd2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2fymc1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	Enolase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2fymc2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2fyma1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Enolase C-terminal domain-like	Enolase	Enolase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2fyma2	Alpha and beta proteins (a+b)	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase N-terminal domain-like	Enolase	(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)
F	SCOP2B Superfamily	Enolase N-terminal domain-like	8041500	3001064	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Enolase N-terminal domain-like	8041500	3001064	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase N-terminal domain-like	8041500	3001064	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2B (2022-06-29)
A	SCOP2 Family	Enolase	8029120	4003240	SCOP2 (2022-06-29)
A	SCOP2 Family	Enolase N-terminal domain-like	8029121	4001209	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Enolase C-terminal domain-like	8041499	3000476	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Enolase N-terminal domain-like	8041500	3001064	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Enolase_N	e2fymF1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Enolase_N	ECOD (v294.1)
F	Meth_synt_2	e2fymF2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)
D	Enolase_N	e2fymD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Enolase_N	ECOD (v294.1)
D	Enolase_C	e2fymD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Enolase_C	ECOD (v294.1)
C	Enolase_N	e2fymC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Enolase_N	ECOD (v294.1)
C	Meth_synt_2	e2fymC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Meth_synt_2	ECOD (v294.1)
A	Enolase_N	e2fymA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Enolase_N	ECOD (v294.1)
A	Enolase_C	e2fymA2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Enolase_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
F	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
D	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
D	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
C	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
C	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)
A	3.30.390.10	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
A	3.20.20.120	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Enolase-like C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, D, F	PF00113	Enolase, C-terminal TIM barrel domain (Enolase_C)	Enolase, C-terminal TIM barrel domain		Domain
A, C, D, F	PF03952	Enolase, N-terminal domain (Enolase_N)	Enolase, N-terminal domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E	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
A, C, D, F	Enolase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity phosphopyruvate hydratase activity catalytic activity carbon-oxygen lyase activity identical protein binding protein binding protein homodimerization activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding hydro-lyase activity lyase activity phosphopyruvate hydratase activity catalytic activity carbon-oxygen lyase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA processing	cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle extracellular region bacterial degradosome exosome (RNase complex) protein-containing complex catalytic complex cytoplasm cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle extracellular region bacterial degradosome exosome (RNase complex) protein-containing complex catalytic complex cytoplasm cytosol cytoplasmic exosome (RNase complex) exoribonuclease complex cell surface phosphopyruvate hydratase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E	IPR028878	Ribonuclease E	Family
B, E	IPR004659	Ribonuclease E/G	Family
B, E	IPR019307	RNA-binding protein AU-1/Ribonuclease E/G	Domain
B, E	IPR003029	S1 domain	Domain
B, E	IPR021968	Polyribonucleotide phosphorylase C-terminal	Domain
B, E	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B, E	IPR048583	RNase E/G, thioredoxin-like domain	Domain
A, C, D, F	IPR036849	Enolase-like, C-terminal domain superfamily	Homologous Superfamily
A, C, D, F	IPR020809	Enolase, conserved site	Conserved Site
A, C, D, F	IPR020810	Enolase, C-terminal TIM barrel domain	Domain
A, C, D, F	IPR020811	Enolase, N-terminal	Domain
A, C, D, F	IPR000941	Enolase	Family
A, C, D, F	IPR029017	Enolase-like, N-terminal	Homologous Superfamily

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.