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Escherichia coli K-12 substr. MG1655 Enzyme: adenylosuccinate lyase



Gene: purB Accession Numbers: EG11314 (EcoCyc), b1131, ECK1117

Synonyms: ade(h), ade

Regulation Summary Diagram: ?

Subunit composition of adenylosuccinate lyase = [PurB]4
         adenylosuccinate lyase = PurB

Summary:
Adenylosuccinate lyase (ASL), the product of the gene purB in E. coli, catalyzes two reactions in de novo purine nucleotide biosynthesis. In addition to the removal of fumarate from 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole, the enzyme also converts adenylosuccinate to AMP [He92].

The enzyme was concluded to be a homotetramer, with a subunit apparent molecular mass of 49.5 kDa determined by SDS-PAGE and a mean native molecular mass of 211 kDa determined by non-denaturing PAGE [Green96]. Crystal structures of the wild-type and mutant enzymes also indicated a homotetramer [Kozlov09, Tsai07]. Note that the PDB link 3GZH ([Kozlov09]) states that the organism is E. coli O157H7, therefore it is shown here as an ortholog. PurB is a member of the aspartase/fumarase superfamily (β-elimination superfamily) [Zhang08e]. The role of His171 in catalysis has been identified [Kozlov09].

An E115K mutation in purB was shown to result in slower growth of E. coli strain DH5α in minimal medium. Replacement with the wild-type allele from E. coli K-12 resulted in an enhanced growth phenotype [Jung10a]. Deletion of purB or purA was shown to result in a decrease in acid resistance, apparently due to the effects of decreased ATP biosynthesis on processes that require ATP for survival under acidic conditions [Sun11a].

Review: [Zhang08e]

Gene Citations: [Meng90]

Locations: cytosol

Map Position: [1,189,839 <- 1,191,209] (25.64 centisomes)
Length: 1371 bp / 456 aa

Molecular Weight of Polypeptide: 51.543 kD (from nucleotide sequence), 49.5 kD (experimental) [Green96 ]

Molecular Weight of Multimer: 211.0 kD (experimental) [Green96]

Unification Links: ASAP:ABE-0003810 , CGSC:344 , EchoBASE:EB1290 , EcoGene:EG11314 , EcoliWiki:b1131 , Mint:MINT-1253735 , ModBase:P0AB89 , OU-Microarray:b1131 , PortEco:purB , PR:PRO_000024882 , Pride:P0AB89 , Protein Model Portal:P0AB89 , RefSeq:NP_415649 , RegulonDB:EG11314 , SMR:P0AB89 , String:511145.b1131 , UniProt:P0AB89

Relationship Links: InterPro:IN-FAMILY:IPR000362 , InterPro:IN-FAMILY:IPR004769 , InterPro:IN-FAMILY:IPR008948 , InterPro:IN-FAMILY:IPR013539 , InterPro:IN-FAMILY:IPR020557 , InterPro:IN-FAMILY:IPR022761 , InterPro:IN-FAMILY:IPR024083 , Panther:IN-FAMILY:PTHR11444 , Panther:IN-FAMILY:PTHR11444:SF2 , Panther:IN-FAMILY:PTHR11444:SF11 , PDB:Structure:2PTQ , PDB:Structure:2PTR , PDB:Structure:2PTS , Pfam:IN-FAMILY:PF00206 , Pfam:IN-FAMILY:PF08328 , Prints:IN-FAMILY:PR00149 , Prosite:IN-FAMILY:PS00163

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0006164 - purine nucleotide biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0006188 - IMP biosynthetic process Inferred by computational analysis [GOA01a]
GO:0006189 - 'de novo' IMP biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0009152 - purine ribonucleotide biosynthetic process Inferred by computational analysis [GOA01a]
GO:0044208 - 'de novo' AMP biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0004018 - N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Green96]
GO:0042802 - identical protein binding Inferred from experiment [Green96]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
GO:0070626 - (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides purine biosynthesis

Essentiality data for purB 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 No 37 Aerobic 7   No [Baba06, Comment 2]

Credits:
Created 19-Dec-2011 by Fulcher C , SRI International
Last-Curated ? 19-Dec-2011 by Fulcher C , SRI International


Enzymatic reaction of: adenylosuccinate lyase

Synonyms: adenylosuccinase, ASL

EC Number: 4.3.2.2

adenylo-succinate <=> fumarate + AMP

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 favored in the direction shown.

In Pathways: superpathway of histidine, purine, and pyrimidine biosynthesis , superpathway of purine nucleotides de novo biosynthesis II , superpathway of adenosine nucleotides de novo biosynthesis II , adenosine ribonucleotides de novo biosynthesis

Kinetic Parameters:

Substrate
Km (μM)
Citations
adenylo-succinate
3.7
[Green96]

pH(opt): 7.4-7.6 [Green96]


Enzymatic reaction of: 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole lyase (adenylosuccinate lyase)

EC Number: 4.3.2.2

5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole <=> fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide

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 favored in the direction shown.

In Pathways: superpathway of histidine, purine, and pyrimidine biosynthesis , superpathway of purine nucleotides de novo biosynthesis II , inosine-5'-phosphate biosynthesis I

Summary:
5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole lyase activity has been demonstrated for the PurB homolog in Bacillus subtilis [Segall04].


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 15 -> 16
[UniProt13]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Protein-Segment 90 -> 92
[UniProt13]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Acetylation-Modification 94
[Zhang09, UniProt11]
UniProt: N6-acetyllysine.
Protein-Segment 122 -> 123
[UniProt13]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Sequence-Conflict 145
[He92, UniProt10]
Alternate sequence: P → A; UniProt: (in Ref. 1; AAA92731);
Sequence-Conflict 154
[He92, UniProt10]
Alternate sequence: I → L; UniProt: (in Ref. 1; AAA92731);
Mutagenesis-Variant 171
[Tsai07, UniProt13]
Alternate sequence: H → N; UniProt: Reduces catalytic activity about 500-fold.
Alternate sequence: H → A; UniProt: Reduces catalytic activity about 500-fold.
Active-Site 171
[Tsai07, UniProt13]
UniProt: Proton donor/acceptor.
Amino-Acid-Sites-That-Bind 247
[UniProt13]
UniProt: Substrate.
Mutagenesis-Variant 295
[Tsai07, UniProt13]
Alternate sequence: S → A; UniProt: Reduces catalytic activity about 1000-fold.
Active-Site 295
[Tsai07, UniProt13]
UniProt: Proton donor/acceptor.
Protein-Segment 301 -> 303
[UniProt13]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 309
[UniProt13]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 335
[UniProt13]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 340
[UniProt13]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Protein-Segment 340 -> 344
[UniProt13]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Acetylation-Modification 366
[Zhang09, UniProt11]
UniProt: N6-acetyllysine.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1131 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11314; confirmed by SwissProt match.


References

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

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."

Green96: Green SM, Malik T, Giles IG, Drabble WT (1996). "The purB gene of Escherichia coli K-12 is located in an operon." Microbiology 1996;142 ( Pt 11);3219-30. PMID: 8969519

He92: He B, Smith JM, Zalkin H (1992). "Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR." J Bacteriol 1992;174(1);130-6. PMID: 1729205

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

Jung10a: Jung SC, Smith CL, Lee KS, Hong ME, Kweon DH, Stephanopoulos G, Jin YS (2010). "Restoration of growth phenotypes of Escherichia coli DH5alpha in minimal media through reversal of a point mutation in purB." Appl Environ Microbiol 76(18);6307-9. PMID: 20675450

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Kozlov09: Kozlov G, Nguyen L, Pearsall J, Gehring K (2009). "The structure of phosphate-bound Escherichia coli adenylosuccinate lyase identifies His171 as a catalytic acid." Acta Crystallogr Sect F Struct Biol Cryst Commun 65(Pt 9);857-61. PMID: 19724117

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

Meng90: Meng LM, Kilstrup M, Nygaard P (1990). "Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli." Eur J Biochem 1990;187(2);373-9. PMID: 2404765

Segall04: Segall ML, Colman RF (2004). "Gln212, Asn270, and Arg301 are critical for catalysis by adenylosuccinate lyase from Bacillus subtilis." Biochemistry 43(23);7391-402. PMID: 15182182

Sun11a: Sun Y, Fukamachi T, Saito H, Kobayashi H (2011). "ATP requirement for acidic resistance in Escherichia coli." J Bacteriol 193(12);3072-7. PMID: 21478347

Tsai07: Tsai M, Koo J, Yip P, Colman RF, Segall ML, Howell PL (2007). "Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism." J Mol Biol 370(3);541-54. PMID: 17531264

UniProt10: 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.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

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."

Zhang08e: Zhang Y, Morar M, Ealick SE (2008). "Structural biology of the purine biosynthetic pathway." Cell Mol Life Sci 65(23);3699-724. PMID: 18712276

Zhang09: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Other References Related to Gene Regulation

Cho11a: Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BO (2011). "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res 39(15);6456-64. PMID: 21572102


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Wed Dec 17, 2014, biocyc13.