4LRZ | pdb_00004lrz

Crystal Structure of the E.coli DhaR(N)-DhaL 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)
D	d4lrzd1	All alpha proteins	DhaL-like	DhaL-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d4lrzd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4lrzc1	All alpha proteins	DhaL-like	DhaL-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4lrzc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4lrzb1	All alpha proteins	DhaL-like	DhaL-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4lrzb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4lrza1	All alpha proteins	DhaL-like	DhaL-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4lrza2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
D	SCOP2B Superfamily	DhaL-like	8088533	3001325	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DhaL-like	8088533	3001325	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DhaL-like	8088533	3001325	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DhaL-like	8088533	3001325	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)
D	preSET_CXC	e4lrzD1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: preSET_CXC	ECOD (develop294)
C	preSET_CXC	e4lrzC1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: preSET_CXC	ECOD (develop294)
B	preSET_CXC	e4lrzB1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: preSET_CXC	ECOD (develop294)
A	PolyA_pol	e4lrzA1	A: alpha bundles	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: PolyA_pol	ECOD (develop294)
H	preSET_CXC	e4lrzH1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: preSET_CXC	ECOD (develop294)
G	preSET_CXC	e4lrzG1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: preSET_CXC	ECOD (develop294)
F	preSET_CXC	e4lrzF1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: preSET_CXC	ECOD (develop294)
E	preSET_CXC	e4lrzE1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: preSET_CXC	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.25.40.340	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	DhaL domain	CATH (4.3.0)
C	1.25.40.340	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	DhaL domain	CATH (4.3.0)
B	1.25.40.340	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	DhaL domain	CATH (4.3.0)
A	1.25.40.340	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	DhaL domain	CATH (4.3.0)
H	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
H	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
G	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
G	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
F	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
F	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
E	3.30.450.40	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	GAF domain	CATH (4.3.0)
E	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, C, D	PF02734	DAK2 domain (Dak2)	DAK2 domain	-	Family
E, F, G, H	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
E, F, G, H	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, C, D	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ADP binding 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	carbohydrate metabolic process polyol metabolic process alcohol catabolic process catabolic process polyol catabolic process carbohydrate catabolic process primary metabolic process alcohol metabolic process alditol catabolic process glycerol metabolic process glycerol catabolic process metabolic process cellular process small molecule metabolic process carbohydrate metabolic process polyol metabolic process alcohol catabolic process catabolic process polyol catabolic process carbohydrate catabolic process primary metabolic process alcohol metabolic process alditol catabolic process glycerol metabolic process glycerol catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process carbohydrate phosphorylation phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process	protein-containing complex catalytic complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
E, F, G, H	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 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 RNA metabolic process positive regulation of RNA biosynthetic process carbohydrate metabolic process polyol 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, C, D	IPR012737	Dihydroxyacetone kinase, subunit L	Domain
A, B, C, D	IPR036117	DhaL domain superfamily	Homologous Superfamily
A, B, C, D	IPR004007	DhaL domain	Domain
A, B, C, D	IPR050861	Dihydroxyacetone Kinase (DAK)	Family
E, F, G, H	IPR013767	PAS fold	Domain
E, F, G, H	IPR009057	Homedomain-like superfamily	Homologous Superfamily
E, F, G, H	IPR058031	NorR-like, AAA+ ATPase lid domain	Domain
E, F, G, H	IPR000014	PAS domain	Domain
E, F, G, H	IPR002197	DNA binding HTH domain, Fis-type	Domain
E, F, G, H	IPR002078	RNA polymerase sigma factor 54 interaction domain	Domain
E, F, G, H	IPR025662	Sigma-54 interaction domain, ATP-binding site 1	Binding Site
E, F, G, H	IPR035965	PAS domain superfamily	Homologous Superfamily
E, F, G, H	IPR003593	AAA+ ATPase domain	Domain
E, F, G, H	IPR003018	GAF domain	Domain
E, F, G, H	IPR029016	GAF-like domain superfamily	Homologous Superfamily
E, F, G, H	IPR025943	Sigma-54 interaction domain, ATP-binding site 2	Binding Site
E, F, G, H	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.