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Escherichia coli K-12 substr. MG1655 Enzyme: argininosuccinate synthase



Gene: argG Accession Numbers: EG10068 (EcoCyc), b3172, ECK3161

Regulation Summary Diagram: ?

Subunit composition of argininosuccinate synthase = [ArgG]4

Summary:
E. coli argininosuccinate synthetase, encoded by the argG gene catalyzes the penultimate step of arginine biosynthesis.

Although enzymological characterization of the E. coli enzyme is lacking, its crystal structure has been determined. The crystal structures of the uncomplexed enzyme and the enzyme in complex with aspartate and citrulline have been determined at 1.6 Å resolution [Lemke01]. The crystal structures of the enzyme in complex with ATP, and with ATP and citrulline, have been determined at 2.0 Å resolution [Lemke02].

The enzyme was present as a monomer in the crystallographic asymmetric unit. However, unpublished analytical gel filtration data for the E. coli enzyme, and biochemical data for the enzyme from mammals and yeast suggest that the enzyme is functional as a tetramer [Lemke01]. The domain structure of the monomer also suggested its ability to form a dimer of dimers [Lemke02]. Each monomer has two structural domains. One is a nucleotide binding domain similar to that of the N-type ATP pyrophosphate class of enzymes, the other is a novel catalytic/multimerization domain. The structural data suggested that citrulline binds at the cleft between the two domains and aspartate binds to a loop of the nucleotide binding domain [Lemke01]. ATP-induced conformational changes in the nucleotide binding domain occur during catalysis [Lemke02].

Based on the crystal structures, the proposed catalytic mechanism involves a two-step reaction. In the first step, the activation of citrulline is brought about by the nucleophilic attack of the ureido oxygen of citrulline on the α-phosphate of ATP, forming citrulline-adenylate. Formation of this intermediate is enhanced in presence of aspartate. In the second step, the ureido carbon of citrulline-adenylate undergoes a nucleophilic attack by the amino group of aspartate, forming argininosuccinate and releasing AMP. There are four active sites per tetramer, each of which comprises residues belonging to a single monomer. A protein conformational change is necessary to bring the citrulline and ATP together for the formation of the adenylated citrulline intermediate [Lemke01].

Locations: cytosol

Map Position: [3,316,659 -> 3,318,002] (71.48 centisomes)
Length: 1344 bp / 447 aa

Molecular Weight of Polypeptide: 49.898 kD (from nucleotide sequence), 50.0 kD (experimental) [Lemke99 ]

Unification Links: ASAP:ABE-0010428 , CGSC:1015 , DIP:DIP-35842N , EchoBASE:EB0066 , EcoGene:EG10068 , EcoliWiki:b3172 , Entrez-gene:947590 , OU-Microarray:b3172 , PortEco:argG , Pride:P0A6E4 , Protein Model Portal:P0A6E4 , RefSeq:NP_417640 , RegulonDB:EG10068 , SMR:P0A6E4 , String:511145.b3172 , UniProt:P0A6E4

Relationship Links: InterPro:IN-FAMILY:IPR001518 , InterPro:IN-FAMILY:IPR014729 , InterPro:IN-FAMILY:IPR018223 , InterPro:IN-FAMILY:IPR023437 , InterPro:IN-FAMILY:IPR024073 , InterPro:IN-FAMILY:IPR024074 , Panther:IN-FAMILY:PTHR11587 , PDB:Structure:1K92 , PDB:Structure:1K97 , PDB:Structure:1KP2 , PDB:Structure:1KP3 , Pfam:IN-FAMILY:PF00764 , Prosite:IN-FAMILY:PS00564 , Prosite:IN-FAMILY:PS00565

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006526 - arginine biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0004055 - argininosuccinate synthase activity Inferred by computational analysis [GOA06, GOA01, GOA01a, Van90]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
GO:0042803 - protein homodimerization activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids arginine

Essentiality data for argG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 5]

Credits:
Last-Curated ? 11-May-2012 by Fulcher C , SRI International


Enzymatic reaction of: argininosuccinate synthase

Synonyms: argininosuccinate synthetase, citrulline-aspartate ligase, L-citrulline:L-aspartate ligase (AMP-forming)

EC Number: 6.3.4.5

L-aspartate + L-citrulline + ATP <=> L-arginino-succinate + AMP + diphosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of arginine and polyamine biosynthesis , arginine biosynthesis I (via L-ornithine)


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Van90, Link97, UniProt11]
UniProt: Removed.
Chain 2 -> 447
[UniProt09]
UniProt: Argininosuccinate synthase;
Nucleotide-Phosphate-Binding-Region 17 -> 25
[UniProt10a]
UniProt: ATP;
Amino-Acid-Sites-That-Bind 43
[UniProt10a]
UniProt: ATP; via amide nitrogen and carbonyl oxygen;
Amino-Acid-Sites-That-Bind 99
[UniProt10a]
UniProt: Citrulline;
Amino-Acid-Sites-That-Bind 129
[UniProt10a]
UniProt: ATP; via amide nitrogen;
Amino-Acid-Sites-That-Bind 131
[UniProt10a]
UniProt: Aspartate;
Amino-Acid-Sites-That-Bind 135
[UniProt10a]
UniProt: Aspartate;
Amino-Acid-Sites-That-Bind 136
[UniProt10a]
UniProt: Aspartate;
Amino-Acid-Sites-That-Bind 139
[UniProt10a]
UniProt: Citrulline;
Amino-Acid-Sites-That-Bind 192
[UniProt10a]
UniProt: Citrulline;
Amino-Acid-Sites-That-Bind 194
[UniProt10a]
UniProt: ATP;
Amino-Acid-Sites-That-Bind 201
[UniProt10a]
UniProt: Citrulline;
Amino-Acid-Sites-That-Bind 203
[UniProt10a]
UniProt: Citrulline;
Sequence-Conflict 220
[Van90, UniProt10a]
Alternate sequence: I → N; UniProt: (in Ref. 1; AAA23482);
Amino-Acid-Sites-That-Bind 280
[UniProt10a]
UniProt: Citrulline;
Sequence-Conflict 328
[Van90, UniProt10a]
Alternate sequence: G → D; UniProt: (in Ref. 1; AAA23482);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3172 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10068; confirmed by SwissProt match.


References

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lemke01: Lemke CT, Howell PL (2001). "The 1.6 A crystal structure of E. coli argininosuccinate synthetase suggests a conformational change during catalysis." Structure 9(12);1153-64. PMID: 11738042

Lemke02: Lemke CT, Howell PL (2002). "Substrate induced conformational changes in argininosuccinate synthetase." J Biol Chem 277(15);13074-81. PMID: 11809762

Lemke99: Lemke C, Yeung M, Howell PL (1999). "Expression, purification, crystallization and preliminary X-ray analysis of Escherichia coli argininosuccinate synthetase." Acta Crystallogr D Biol Crystallogr 1999;55 ( Pt 12);2028-30. PMID: 10666579

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Van90: Van Vliet F, Crabeel M, Boyen A, Tricot C, Stalon V, Falmagne P, Nakamura Y, Baumberg S, Glansdorff N (1990). "Sequences of the genes encoding argininosuccinate synthetase in Escherichia coli and Saccharomyces cerevisiae: comparison with methanogenic archaebacteria and mammals." Gene 1990;95(1);99-104. PMID: 2123815

Other References Related to Gene Regulation

Caldara06: Caldara M, Charlier D, Cunin R (2006). "The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation." Microbiology 152(Pt 11);3343-54. PMID: 17074904

Charlier92: Charlier D, Roovers M, Van Vliet F, Boyen A, Cunin R, Nakamura Y, Glansdorff N, Pierard A (1992). "Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression." J Mol Biol 1992;226(2);367-86. PMID: 1640456

Krin03: Krin E, Laurent-Winter C, Bertin PN, Danchin A, Kolb A (2003). "Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12." J Bacteriol 185(10);3139-46. PMID: 12730174

Makarova01: Makarova KS, Mironov AA, Gelfand MS (2001). "Conservation of the binding site for the arginine repressor in all bacterial lineages." Genome Biol 2(4);RESEARCH0013. PMID: 11305941

Shimada13: Shimada T, Yoshida H, Ishihama A (2013). "Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli." J Bacteriol 195(10);2212-9. PMID: 23475967


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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