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Escherichia coli K-12 substr. MG1655 Enzyme: aspartate semialdehyde dehydrogenase



Gene: asd Accession Numbers: EG10088 (EcoCyc), b3433, ECK3419

Synonyms: dap, hom

Regulation Summary Diagram: ?

Subunit composition of aspartate semialdehyde dehydrogenase = [Asd]2

Summary:
Aspartate semialdehyde dehydrogenase (Asd) carries out the middle step in the pathway of homoserine biosynthesis, generating L-aspartate-semialdehyde.

Asd catalyzes the NADPH-dependent conversion of L-aspartyl-4-phosphate to L-aspartate-semialdehyde [Boy72, Biellmann80, Alvarez04, Haziza82, Cohen85]. As AsD transfers the pro-S hydrogen from NADPH, it is a class B hydrogenase [Biellmann80].

Aspartate semialdehyde dehydrogenase comprises a dimer of Asd monomers [Biellmann80]. A number of crystal structures have been solved for Asd, in both active and inactive forms [Thierry80, Kryger92, Nichols04]. A crystal structure to 2.5 Å resolution shows that each Asd monomer has an amino-terminal NADPH-binding domain and a separate dimerization domain, with the active site existing in a cleft between the two domains [Hadfield99]. The active site contains a cysteine, Cys-135, that is required for activity, but reportedly not for substrate binding [Karsten92]. A crystal structure with a substrate analog, however, shows that it binds to this cysteine [Hadfield01].

As observed in extract, the activity of Asd appears to undergo short-term repression by lysine, methionine, and threonine [Boy72].

Locations: cytosol

Map Position: [3,571,798 <- 3,572,901] (76.98 centisomes)
Length: 1104 bp / 367 aa

Molecular Weight of Polypeptide: 40.018 kD (from nucleotide sequence), 38.0 kD (experimental) [Biellmann80 ]

Molecular Weight of Multimer: 77.0 kD (experimental) [Biellmann80]

pI: 4.3 [Biellmann80]

Unification Links: ASAP:ABE-0011211 , CGSC:996 , EchoBASE:EB0086 , EcoGene:EG10088 , EcoliWiki:b3433 , ModBase:P0A9Q9 , OU-Microarray:b3433 , PortEco:asd , PR:PRO_000022164 , Pride:P0A9Q9 , Protein Model Portal:P0A9Q9 , RefSeq:NP_417891 , RegulonDB:EG10088 , SMR:P0A9Q9 , String:511145.b3433 , UniProt:P0A9Q9

Relationship Links: InterPro:IN-FAMILY:IPR000319 , InterPro:IN-FAMILY:IPR000534 , InterPro:IN-FAMILY:IPR011534 , InterPro:IN-FAMILY:IPR012080 , InterPro:IN-FAMILY:IPR012280 , InterPro:IN-FAMILY:IPR016040 , PDB:Structure:1BRM , PDB:Structure:1GL3 , PDB:Structure:1T4B , PDB:Structure:1T4D , Pfam:IN-FAMILY:PF01118 , Pfam:IN-FAMILY:PF02774 , Prosite:IN-FAMILY:PS01103 , Smart:IN-FAMILY:SM00859

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0009089 - lysine biosynthetic process via diaminopimelate Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA01a, Alvarez04]
GO:0009090 - homoserine biosynthetic process Inferred from experiment [Alvarez04]
GO:0006520 - cellular amino acid metabolic process Inferred by computational analysis [GOA01a]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0009085 - lysine biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0009086 - methionine biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0009088 - threonine biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a]
GO:0009097 - isoleucine biosynthetic process Inferred by computational analysis [GOA01a]
GO:0019877 - diaminopimelate biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0071266 - 'de novo' L-methionine biosynthetic process Inferred by computational analysis [GOA06]
Molecular Function: GO:0004073 - aspartate-semialdehyde dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Alvarez04]
GO:0003942 - N-acetyl-gamma-glutamyl-phosphate reductase activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01a]
GO:0046983 - protein dimerization activity Inferred by computational analysis [GOA01a]
GO:0050661 - NADP binding Inferred by computational analysis [GOA06, GOA01a]
GO:0051287 - NAD binding 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 [GOA01a]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids homoserine
metabolism biosynthesis of building blocks amino acids lysine

Essentiality data for asd knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Credits:
Last-Curated ? 15-Aug-2007 by Shearer A , SRI International


Enzymatic reaction of: aspartate semialdehyde dehydrogenase

Synonyms: L-Aspartate-4-semialdehyde:NADP+ oxidoreductase (phosphorylating), Aspartate-β-semialdehyde dehydrogenase, ASA-dehydrogenase

EC Number: 1.2.1.11

L-aspartate-semialdehyde + NADP+ + phosphate <=> L-aspartyl-4-phosphate + NADPH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

In Pathways: superpathway of S-adenosyl-L-methionine biosynthesis , homoserine and methionine biosynthesis , threonine biosynthesis , superpathway of lysine, threonine and methionine biosynthesis I , aspartate superpathway , homoserine biosynthesis , lysine biosynthesis I

Summary:
L-2-amino-4-oxo-5-chloropentanoic acid is an irreversible competitive inhibitor that binds the active-site cysteine [Biellmann80a]. Glutathione is an inhibitor in its oxidized state [Alvarez04].

Inhibitors (Competitive): L-2-amino-4-oxo-5-chloropentanoate [Biellmann80a]

Inhibitors (Noncompetitive): p-hydroxymercuribenzoate [Hegeman70, Helmward89] , N-ethylmaleimide [Hegeman70, Helmward89] , iodoacetate [Hegeman70, Helmward89]

Inhibitors (Unknown Mechanism): tris [Helmward89, Hegeman70] , glutathione [Alvarez04] , 5,5'-dithio-bis-2-nitrobenzoate [Alvarez04] , K+ [Hegeman70, Helmward89] , Na+ [Helmward89, Hegeman70] , ammonium [Helmward89, Hegeman70] , borate [Helmward89, Hegeman70] , L-cystine [Alvarez04]

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-aspartate-semialdehyde
110.0
[Chassagnole01]
NADP+
144.0
[Chassagnole01]
phosphate
2900.0
[Kish99, BRENDA14]
phosphate
10000.0
[Chassagnole01]
L-aspartyl-4-phosphate
22.0
[Chassagnole01]
NADPH
29.0
[Chassagnole01]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 9
[Link97, UniProt10a]
Alternate sequence: W → G; UniProt: (in Ref. 4; AA sequence);
Nucleotide-Phosphate-Binding-Region 10 -> 13
[UniProt11]
UniProt: NADP.
Nucleotide-Phosphate-Binding-Region 37 -> 38
[UniProt11]
UniProt: NADP.
Amino-Acid-Sites-That-Bind 73
[UniProt11]
UniProt: NADP.
Amino-Acid-Sites-That-Bind 102
[UniProt11]
UniProt: Phosphate; Non-Experimental Qualifier: by similarity.
S-cysteinyl-cysteine-Modification 135
[UniProt11]
UniProt: S-cysteinyl cysteine; in inhibited form.
Mutagenesis-Variant 135
[Karsten92, UniProt11a]
Alternate sequence: C → S; UniProt: 99.7% loss of activity.
Alternate sequence: C → A; UniProt: Complete loss of activity.
Active-Site 135
[Hadfield01, Karsten92, Biellmann80a, Ouyang95]
This cysteine is required for activity, and may be involved in directly binding substrate.
Amino-Acid-Sites-That-Bind 162
[UniProt11]
UniProt: Substrate.
Nucleotide-Phosphate-Binding-Region 165 -> 169
[UniProt11]
UniProt: NADP.
Amino-Acid-Sites-That-Bind 173
[UniProt11]
UniProt: NADP.
Amino-Acid-Sites-That-Bind 193
[UniProt11]
UniProt: NADP; via carbonyl oxygen.
Acetylation-Modification 232
[Yu08]
 
Amino-Acid-Sites-That-Bind 241
[UniProt11]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 244
[UniProt11]
UniProt: Phosphate; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 267
[UniProt11]
UniProt: Substrate.
Active-Site 274
[Hadfield01, Karsten92, UniProt11]
UniProt: Proton acceptor.
Amino-Acid-Sites-That-Bind 350
[UniProt11]
UniProt: NADP.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3433 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10088; confirmed by SwissProt match.


References

Alvarez04: Alvarez E, Ramon F, Magan C, Diez E (2004). "L-cystine inhibits aspartate-beta-semialdehyde dehydrogenase by covalently binding to the essential 135Cys of the enzyme." Biochim Biophys Acta 1696(1);23-9. PMID: 14726201

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

Biellmann80: Biellmann JF, Eid P, Hirth C, Jornvall H (1980). "Aspartate-beta-semialdehyde dehydrogenase from Escherichia coli. Purification and general properties." Eur J Biochem 1980;104(1);53-8. PMID: 6102909

Biellmann80a: Biellmann JF, Eid P, Hirth C (1980). "Affinity labeling of the Escherichia coli aspartate-beta-semialdehyde dehydrogenase with an alkylating coenzyme analogue. Half-site reactivity and competition with the substrate alkylating analogue." Eur J Biochem 1980;104(1);65-9. PMID: 6102911

Boy72: Boy E, Patte JC (1972). "Multivalent repression of aspartic semialdehyde dehydrogenase in Escherichia coli K-12." J Bacteriol 112(1);84-92. PMID: 4404058

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Chassagnole01: Chassagnole C, Rais B, Quentin E, Fell DA, Mazat JP (2001). "An integrated study of threonine-pathway enzyme kinetics in Escherichia coli." Biochem J 356(Pt 2);415-23. PMID: 11368768

Cohen85: Cohen GN (1985). "Aspartate-semialdehyde dehydrogenase from Escherichia coli." Methods Enzymol 113;600-2. PMID: 2868399

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

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."

Hadfield01: Hadfield A, Shammas C, Kryger G, Ringe D, Petsko GA, Ouyang J, Viola RE (2001). "Active site analysis of the potential antimicrobial target aspartate semialdehyde dehydrogenase." Biochemistry 40(48);14475-83. PMID: 11724560

Hadfield99: Hadfield A, Kryger G, Ouyang J, Petsko GA, Ringe D, Viola R (1999). "Structure of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis." J Mol Biol 289(4);991-1002. PMID: 10369777

Haziza82: Haziza C, Stragier P, Patte JC (1982). "Nucleotide sequence of the asd gene of Escherichia coli: absence of a typical attenuation signal." EMBO J 1982;1(3);379-84. PMID: 6143662

Hegeman70: Hegeman G, Cohen G, Morgan R "Aspartic semialdehyde dehydrogenase (Escherichia coli K12)." Methods in Enzymology 1970; 17A:708-713.

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

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

Karsten92: Karsten WE, Viola RE (1992). "Identification of an essential cysteine in the reaction catalyzed by aspartate-beta-semialdehyde dehydrogenase from Escherichia coli." Biochim Biophys Acta 1121(1-2);234-8. PMID: 1350921

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

Kish99: Kish MM, Viola RE (1999). "Oxyanion Specificity of Aspartate-beta-semialdehyde Dehydrogenase." Inorg Chem 38(4);818-820. PMID: 11670848

Kryger92: Kryger G, Petsko GA, Ouyang J, Viola RE (1992). "Crystallization and preliminary crystallographic analysis of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli." J Mol Biol 1992;228(1);300-1. PMID: 1360028

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

Nichols04: Nichols CE, Dhaliwal B, Lockyer M, Hawkins AR, Stammers DK (2004). "High-resolution structures reveal details of domain closure and "half-of-sites-reactivity" in Escherichia coli aspartate beta-semialdehyde dehydrogenase." J Mol Biol 341(3);797-806. PMID: 15288787

Ouyang95: Ouyang J, Viola RE (1995). "Use of structural comparisons to select mutagenic targets in aspartate-beta-semialdehyde dehydrogenase." Biochemistry 34(19);6394-9. PMID: 7756269

Thierry80: Thierry JC, Moras D, Eid P, Hirth C (1980). "Crystallization of E. coli aspartate beta-semialdehyde dehydrogenase." Biochimie 62(10);739-40. PMID: 6108787

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Other References Related to Gene Regulation

Marbaniang11: Marbaniang CN, Gowrishankar J (2011). "Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli." J Bacteriol 193(21);5985-96. PMID: 21890697


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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 Sat Dec 20, 2014, BIOCYC13B.