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Escherichia coli K-12 substr. MG1655 Enzyme: L-serine deaminase I



Gene: sdaA Accession Numbers: EG10930 (EcoCyc), b1814, ECK1812

Synonyms: SDH1, L-SD, SDH-1, L-SD1

Regulation Summary Diagram: ?

Summary:
L-serine deaminase I (SdaA) is one of three enzymes carrying out the sole step in the pathway of L-serine degradation, converting serine into a basic cellular building block, pyruvate.

SdaA catalyzes the conversion of L-serine into pyruvate and ammonia [Su89, Su93, Cicchillo04].

SdaA contains a catalytically critical 4Fe-4S cluster that interacts directly with the L-serine substrate [Cicchillo04]. This cluster is only present when the enzyme is synthesized under anaerobic conditions [Su89, Su93]. Oxidatively inactivated serine deaminase can be activated in vitro with a combination of iron sulfate and dithiothreitol [Newman85, Su93, Cicchillo04]. Activation in vivo, presumably involving construction of the 4Fe-4S cluster, appears to require multiple additional gene products [Newman85].

Gene Citations: [Fraenkel95]

Locations: cytosol

Map Position: [1,894,956 -> 1,896,320] (40.84 centisomes)
Length: 1365 bp / 454 aa

Molecular Weight of Polypeptide: 48.907 kD (from nucleotide sequence)

pI: 5.4

Isozyme Sequence Similarity:
L-serine deaminase III: YES ,
L-serine deaminase II: YES

Unification Links: ASAP:ABE-0006039 , CGSC:32312 , EchoBASE:EB0923 , EcoGene:EG10930 , EcoliWiki:b1814 , OU-Microarray:b1814 , PortEco:sdaA , PR:PRO_000023915 , Pride:P16095 , Protein Model Portal:P16095 , RefSeq:NP_416328 , RegulonDB:EG10930 , SMR:P16095 , String:511145.b1814 , UniProt:P16095

Relationship Links: InterPro:IN-FAMILY:IPR004644 , InterPro:IN-FAMILY:IPR005130 , InterPro:IN-FAMILY:IPR005131 , Pfam:IN-FAMILY:PF03313 , Pfam:IN-FAMILY:PF03315

In Paralogous Gene Group: 458 (6 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006565 - L-serine catabolic process Inferred from experiment [Cicchillo04]
GO:0006094 - gluconeogenesis Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA01]
Molecular Function: GO:0003941 - L-serine ammonia-lyase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Cicchillo04]
GO:0005515 - protein binding Inferred from experiment [Zheng11]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08]

MultiFun Terms: metabolism carbon utilization amino acids

Essentiality data for sdaA 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 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 18-Sep-2007 by Shearer A , SRI International


Enzymatic reaction of: L-serine deaminase

Synonyms: L-serine dehydratase, L-hydroxyaminoacid dehydratase, L-serine hydro-lyase (deaminating), L-serine ammonia-lyase

L-serine <=> 2-aminoprop-2-enoate + H+ + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: L-serine degradation

Summary:
D-serine inhibits with a Ki of 1.41 mM, and L-cysteine inhibits with a Ki of 0.9 mM [Cicchillo04].

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Cicchillo04]

Inhibitors (Unknown Mechanism): Zn2+ [Newman80a] , Cu2+ [Newman80a] , L-cysteine [Cicchillo04] , D-serine [Newman80a, Cicchillo04] , ethanolamine [Newman80a] , o-phenanthroline [Newman80a]

Primary Physiological Regulators of Enzyme Activity: L-cysteine , D-serine

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-serine
420000.0
[Newman80a, BRENDA14]
L-serine
2670.0
436.0
[Cicchillo04, BRENDA14]
L-serine
4800.0
544.0
[Burman04, BRENDA14]

T(opt): 37 °C [BRENDA14, Anfora07]


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1814 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10930; confirmed by SwissProt match.


References

Anfora07: Anfora AT, Haugen BJ, Roesch P, Redford P, Welch RA (2007). "Roles of serine accumulation and catabolism in the colonization of the murine urinary tract by Escherichia coli CFT073." Infect Immun 75(11);5298-304. PMID: 17785472

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

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

Burman04: Burman JD, Harris RL, Hauton KA, Lawson DM, Sawers RG (2004). "The iron-sulfur cluster in the L-serine dehydratase TdcG from Escherichia coli is required for enzyme activity." FEBS Lett 576(3);442-4. PMID: 15498577

Cicchillo04: Cicchillo RM, Baker MA, Schnitzer EJ, Newman EB, Krebs C, Booker SJ (2004). "Escherichia coli L-serine deaminase requires a [4Fe-4S] cluster in catalysis." J Biol Chem 279(31);32418-25. PMID: 15155761

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

Fraenkel95: Fraenkel YM, Mandel Y, Friedberg D, Margalit H (1995). "Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon." Comput Appl Biosci 1995;11(4);379-87. PMID: 8521047

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

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Newman80a: Newman EB, Kapoor V (1980). "In vitro studies on L-serine deaminase activity of Escherichia coli K12." Can J Biochem 1980;58(11);1292-7. PMID: 7011505

Newman85: Newman EB, Dumont D, Walker C (1985). "In vitro and in vivo activation of L-serine deaminase in Escherichia coli K-12." J Bacteriol 1985;162(3);1270-5. PMID: 3888962

Su89: Su HS, Lang BF, Newman EB (1989). "L-serine degradation in Escherichia coli K-12: cloning and sequencing of the sdaA gene." J Bacteriol 171(9);5095-102. PMID: 2504697

Su93: Su H, Moniakis J, Newman EB (1993). "Use of gene fusions of the structural gene sdaA to purify L-serine deaminase 1 from Escherichia coli K-12." Eur J Biochem 1993;211(3);521-7. PMID: 8436113

UniProtGOA11: 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."

Zheng11: Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE (2011). "Cross-linking measurements of in vivo protein complex topologies." Mol Cell Proteomics 10(10);M110.006841. PMID: 21697552

Other References Related to Gene Regulation

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065


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 Fri Nov 28, 2014, BIOCYC14A.