6C8Q | pdb_00006c8q

Crystal structure of NAD synthetase (NadE) from Enterococcus faecalis in complex with NAD+

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	d6c8qa_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	automated matches	automated matches	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
C	d6c8qc_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	automated matches	automated matches	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
D	d6c8qd_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	automated matches	automated matches	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
F	d6c8qf_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	automated matches	automated matches	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
H	d6c8qh_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	automated matches	automated matches	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
G	d6c8qg_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	automated matches	automated matches	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
E	d6c8qe_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	automated matches	automated matches	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
B	d6c8qb_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	automated matches	automated matches	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	N-type ATP pyrophosphatases	8073604	4003831	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Adenine nucleotide alpha hydrolases-like	8073605	3001593	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8073605	3001593	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8073605	3001593	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8073605	3001593	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8073605	3001593	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8073605	3001593	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8073605	3001593	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8073605	3001593	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	SAM_KSR1_N	e6c8qA1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
C	SAM_KSR1_N	e6c8qC1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
D	SAM_KSR1_N	e6c8qD1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
F	SAM_KSR1_N	e6c8qF1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
H	SAM_KSR1_N	e6c8qH1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
G	SAM_KSR1_N	e6c8qG1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
E	SAM_KSR1_N	e6c8qE1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
B	14-3-3	e6c8qB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: 14-3-3	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
D	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
F	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
H	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
G	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
E	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF02540	NAD synthase (NAD_synthase)	NAD synthase	NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	NH(3)-dependent NAD(+) synthetase	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 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 NAD+ synthase (glutamine-hydrolyzing) activity carbon-nitrogen ligase activity, with glutamine as amido-N-donor catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides glutaminase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding metal ion binding acid-ammonia (or amide) ligase activity NAD+ synthase activity	NAD+ biosynthetic process nucleotide biosynthetic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process NAD+ metabolic process pyridine nucleotide biosynthetic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process NAD+ biosynthetic process nucleotide biosynthetic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process NAD+ metabolic process pyridine nucleotide biosynthetic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyridine-containing compound biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nicotinamide nucleotide biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine nucleotide biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022310	NAD/GMP synthase	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022926	NH(3)-dependent NAD(+) synthetase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003694	NAD(+) synthetase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	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.