4LRY | pdb_00004lry

Crystal Structure of the E.coli DhaR(N)-DhaK(T79L) complex

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	d4lrya_	Alpha and beta proteins (a/b)	DAK1/DegV-like	DAK1/DegV-like	DAK1	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4lryb_	Alpha and beta proteins (a/b)	DAK1/DegV-like	DAK1/DegV-like	DAK1	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DAK1/DegV-like	8037867	3000337	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DAK1/DegV-like	8037867	3000337	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	Dak1_C	e4lryA1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: DAK1/DegV C-terminal domain (From Topology)	T: DAK1/DegV C-terminal domain	F: Dak1_C	ECOD (1.6)
A	Dak1_N	e4lryA2	A: a/b three-layered sandwiches	X: EDD domain (From Topology)	H: EDD domain (From Topology)	T: EDD domain	F: Dak1_N	ECOD (1.6)
B	Dak1_C	e4lryB2	A: a+b three layers	X: Bacillus chorismate mutase-like	H: DAK1/DegV C-terminal domain (From Topology)	T: DAK1/DegV C-terminal domain	F: Dak1_C	ECOD (1.6)
B	Dak1_N	e4lryB1	A: a/b three-layered sandwiches	X: EDD domain (From Topology)	H: EDD domain (From Topology)	T: EDD domain	F: Dak1_N	ECOD (1.6)
C	PAS_1	e4lryC1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_1	ECOD (1.6)
C	UNK_F_TYPE	e4lryC2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: UNK_F_TYPE	ECOD (1.6)
D	PAS_1	e4lryD1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_1	ECOD (1.6)
D	UNK_F_TYPE	e4lryD2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dihydroxyacetone kinase	CATH (4.3.0)
A	3.30.1180.20	Alpha Beta	2-Layer Sandwich	Hypothetical Protein Tm841	Chain: A	CATH (4.3.0)
B	3.40.50.10440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dihydroxyacetone kinase	CATH (4.3.0)
B	3.30.1180.20	Alpha Beta	2-Layer Sandwich	Hypothetical Protein Tm841	Chain: A	CATH (4.3.0)
C	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
C	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
D	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
D	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02733	Dak1 domain (Dak1)	Dak1 domain	-	Family
C, D	PF01590	GAF domain (GAF)	GAF domain	This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regul ...	This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
C, D	PF00989	PAS fold (PAS)	PAS fold	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ [5 ...	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity kinase activity glycerone kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups phosphoenolpyruvate-glycerone phosphotransferase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process ketone metabolic process ketone catabolic process metabolic process small molecule metabolic process small molecule catabolic process carbohydrate metabolic process polyol metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process ketone metabolic process ketone catabolic process metabolic process small molecule metabolic process small molecule catabolic process carbohydrate metabolic process polyol metabolic process alcohol catabolic process polyol catabolic process carbohydrate catabolic process primary metabolic process alcohol metabolic process alditol catabolic process glycerol metabolic process alditol metabolic process glycerol catabolic process monosaccharide metabolic process monosaccharide catabolic process pyruvate metabolic process oxoacid metabolic process carboxylic acid metabolic process monocarboxylic acid metabolic process organic acid metabolic process carbohydrate derivative metabolic process organophosphate metabolic process phosphate-containing compound metabolic process glycerol to glycerone phosphate metabolic process phosphorus metabolic process primary alcohol metabolic process carbohydrate phosphorylation phosphorylation	protein-containing complex catalytic complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
C, D	PTS-dependent dihydroxyacetone kinase operon regulatory protein	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 DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process carbohydrate metabolic process polyol metabolic process alditol metabolic process alcohol metabolic process small molecule metabolic process glycerol metabolic process	protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004006	DhaK domain	Domain
A, B	IPR012736	Dihydroxyacetone kinase DhaK, subunit 1	Domain
A, B	IPR050861	Dihydroxyacetone Kinase (DAK)	Family
C, D	IPR013767	PAS fold	Domain
C, D	IPR009057	Homedomain-like superfamily	Homologous Superfamily
C, D	IPR000014	PAS domain	Domain
C, D	IPR002197	DNA binding HTH domain, Fis-type	Domain
C, D	IPR002078	RNA polymerase sigma factor 54 interaction domain	Domain
C, D	IPR025662	Sigma-54 interaction domain, ATP-binding site 1	Binding Site
C, D	IPR035965	PAS domain superfamily	Homologous Superfamily
C, D	IPR003593	AAA+ ATPase domain	Domain
C, D	IPR003018	GAF domain	Domain
C, D	IPR029016	GAF-like domain superfamily	Homologous Superfamily
C, D	IPR025943	Sigma-54 interaction domain, ATP-binding site 2	Binding Site
C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.