Summary: Arginine repressor, C-terminal domain
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|Arginine repressor, C-terminal domain|
c-terminal domain of escherichia coli arginine repressor/ l-arginine complex; pb derivative
|Arginine repressor, DNA binding domain|
In molecular biology, the arginine repressor (ArgR) is a repressor of prokaryotic arginine deiminase pathways.
The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis). The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein.
Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region.
- Brown DM, Upcroft JA, Edwards MR, Upcroft P (January 1998). "Anaerobic bacterial metabolism in the ancient eukaryote Giardia duodenalis". Int. J. Parasitol. 28 (1): 149–64. doi:10.1016/S0020-7519(97)00172-0. PMID 9504342.
- Lu CD, Houghton JE, Abdelal AT (May 1992). "Characterization of the arginine repressor from Salmonella typhimurium and its interactions with the carAB operator". J. Mol. Biol. 225 (1): 11–24. doi:10.1016/0022-2836(92)91022-H. PMID 1583685.
- Maghnouj A, de Sousa Cabral TF, Stalon V, Vander Wauven C (December 1998). "The arcABDC gene cluster, encoding the arginine deiminase pathway of Bacillus licheniformis, and its activation by the arginine repressor argR". J. Bacteriol. 180 (24): 6468–75. PMC 107747. PMID 9851988.
- Ni J, Sakanyan V, Charlier D, Glansdorff N, Van Duyne GD (May 1999). "Structure of the arginine repressor from Bacillus stearothermophilus". Nat. Struct. Biol. 6 (5): 427–32. doi:10.1038/8229. PMID 10331868.
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Sunnerhagen M, Nilges M, Otting G, Carey J; , Nat Struct Biol 1997;4:819-826.: Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA. PUBMED:9334747 EPMC:9334747
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This tab holds annotation information from the InterPro database.
InterPro entry IPR020899
The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) [PUBMED:9504342]. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein [PUBMED:9504342].
Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR [PUBMED:1583685]. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine [PUBMED:9851988]. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography [PUBMED:10331868]. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region.The C-terminal domain of the arginine repressor is responsible for aginine binding and multimerisation [PUBMED:11856827, PUBMED:9334747].
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|Molecular function||arginine binding (GO:0034618)|
|Biological process||protein oligomerization (GO:0051259)|
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|Seed source:||Sarah Teichmann|
|Author:||Finn RD, Bateman A, Griffiths-Jones SR|
|Number in seed:||146|
|Number in full:||4296|
|Average length of the domain:||69.90 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||45.54 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Arg_repressor_C domain has been found. There are 74 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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