3A5Z

Crystal structure of Escherichia coli GenX in complex with elongation factor P

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)
B	d3a5zb1	All beta proteins	SH3-like barrel	Translation proteins SH3-like domain	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3a5zb2	All beta proteins	OB-fold	Nucleic acid-binding proteins	automated matches	automated matches	(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	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8098374	3000058	SCOP2B (2022-06-29)
C	SCOP2 Family	Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	8098373	4001782	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Class II aaRS and biotin synthetases	8098374	3000058	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8098374	3000058	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8098374	3000058	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	tRNA-synt_2	e3a5zA1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2	ECOD (1.6)
C	tRNA-synt_2	e3a5zC1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2	ECOD (1.6)
G	tRNA-synt_2	e3a5zG1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2	ECOD (1.6)
E	tRNA-synt_2	e3a5zE1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2	ECOD (1.6)
B	EFP	e3a5zB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: EFP	ECOD (1.6)
B	EFP_N	e3a5zB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EFP_N	ECOD (1.6)
F	EFP_N	e3a5zF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EFP_N	ECOD (1.6)
H	EFP	e3a5zH1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: EFP	ECOD (1.6)
H	Elong-fact-P_C	e3a5zH2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Elong-fact-P_C	ECOD (1.6)
H	EFP_N	e3a5zH3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EFP_N	ECOD (1.6)
D	EFP	e3a5zD1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: EFP	ECOD (1.6)
D	Elong-fact-P_C	e3a5zD2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Elong-fact-P_C	ECOD (1.6)
D	EFP_N	e3a5zD3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EFP_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
C	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
G	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
E	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
F	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
H	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
H	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF00152	tRNA synthetases class II (D, K and N) (tRNA-synt_2)	tRNA synthetases class II (D, K and N)	-	Domain
B, D, F, H	PF09285	Elongation factor P, C-terminal (Elong-fact-P_C)	Elongation factor P, C-terminal	Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology [1].	Domain
B, D, F, H	PF01132	Elongation factor P (EF-P) OB domain (EFP)	Elongation factor P (EF-P) OB domain	-	Domain
B, D, F, H	PF08207	Elongation factor P (EF-P) KOW-like domain (EFP_N)	Elongation factor P (EF-P) KOW-like domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Putative lysyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA lysine-tRNA ligase activity catalytic activity ligase activity acid-ammonia (or amide) ligase activity ligase activity, forming carbon-nitrogen bonds aminoacyltransferase activity protein-lysine lysyltransferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity RNA binding tRNA binding nucleic acid binding	cellular response to stimulus response to stimulus response to pH cellular response to pH response to abiotic stimulus cellular process cellular response to acidic pH cellular response to abiotic stimulus response to acidic pH cellular response to environmental stimulus lysyl-tRNA aminoacylation amino acid activation tRNA aminoacylation cellular biosynthetic process cellular response to stimulus response to stimulus response to pH cellular response to pH response to abiotic stimulus cellular process cellular response to acidic pH cellular response to abiotic stimulus response to acidic pH cellular response to environmental stimulus lysyl-tRNA aminoacylation amino acid activation tRNA aminoacylation cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process metabolic process macromolecule metabolic process protein metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol
B, D, F, H	Elongation factor P	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding	peptide biosynthetic process biosynthetic process metabolic process peptide metabolic process cellular component disassembly ribosome disassembly cellular biosynthetic process cellular metabolic process rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization peptide biosynthetic process biosynthetic process metabolic process peptide metabolic process cellular component disassembly ribosome disassembly cellular biosynthetic process cellular metabolic process rescue of stalled ribosome primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization organelle organization organelle disassembly translational elongation cellular process cellular component organization or biogenesis macromolecule metabolic process protein metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process regulation of translational frameshifting post-transcriptional regulation of gene expression regulation of translational elongation negative regulation of translation negative regulation of cellular process negative regulation of translational frameshifting translational frameshifting negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of translational elongation negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, C, E, G	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, C, E, G	IPR018149	Lysyl-tRNA synthetase, class II, C-terminal	Domain
A, C, E, G	IPR004364	Aminoacyl-tRNA synthetase, class II (D/K/N)	Domain
A, C, E, G	IPR004525	Elongation factor P--(R)-beta-lysine ligase	Family
B, D, F, H	IPR020599	Translation elongation factor P/YeiP	Family
B, D, F, H	IPR015365	Elongation factor P, C-terminal	Domain
B, D, F, H	IPR013185	Translation elongation factor, KOW-like	Domain
B, D, F, H	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
B, D, F, H	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
B, D, F, H	IPR001059	Translation elongation factor P/YeiP, central	Domain
B, D, F, H	IPR011768	Translation elongation factor P	Family
B, D, F, H	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B, D, F, H	IPR013852	Translation elongation factor P/YeiP, 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.