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



Gene: sdaB Accession Numbers: EG11623 (EcoCyc), b2797, ECK2792

Synonyms: SDH-2, L-SD2

Regulation Summary Diagram: ?

Summary:
L-serine deaminase II (SdaB) 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.

SdaB catalyzes the conversion of L-serine into pyruvate and ammonia [Su91].

Much like its companion enzyme L-serine deaminase I, purified SdaB requires activation in vitro with iron and dithiothrietol, suggesting that it, too, has a catalytically important iron-sulfur cluster [Su91].

Like fellow serine deaminase gene tdcG, sdaB is transcribed under glucose-limited conditions in complex medium [Shao93a].
By making use of micro arrays analysis it was concluded that anarobiosis do not affect the expression of the sdaB gene, although FNR appears to activate it. A putative FNR binding site, which is not shown in the paper, was identified upstream of this operon [Salmon03].

Gene Citations: [Shao94]

Map Position: [2,927,598 -> 2,928,965] (63.1 centisomes)
Length: 1368 bp / 455 aa

Molecular Weight of Polypeptide: 48.753 kD (from nucleotide sequence)

pI: 5.7

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

Unification Links: ASAP:ABE-0009172 , CGSC:33324 , EchoBASE:EB1580 , EcoGene:EG11623 , EcoliWiki:b2797 , OU-Microarray:b2797 , PortEco:sdaB , PR:PRO_000023916 , Pride:P30744 , Protein Model Portal:P30744 , RefSeq:NP_417277 , RegulonDB:EG11623 , SMR:P30744 , String:511145.b2797 , UniProt:P30744

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

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006565 - L-serine catabolic process Inferred from experiment [Su91]
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, Su91]
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]

MultiFun Terms: metabolism carbon utilization amino acids

Essentiality data for sdaB 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 <=> 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

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Su91]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-serine
420000.0
[Newman80, BRENDA14]
L-serine
2670.0
436.0
[Cicchillo04, BRENDA14]
L-serine
4800.0
544.0
[Burman04, BRENDA14]

T(opt): 37 °C [BRENDA14, Anfora07]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 132
[Shao93a, UniProt10]
Alternate sequence: L → V; UniProt: (in Ref. 1);
Sequence-Conflict 134
[Shao93a, UniProt10]
Alternate sequence: G → A; UniProt: (in Ref. 1);
Sequence-Conflict 196 -> 197
[Shao93a, UniProt10]
Alternate sequence: EL → DV; UniProt: (in Ref. 1);
Sequence-Conflict 236 -> 239
[Shao93a, UniProt10]
Alternate sequence: VPRR → STPC; UniProt: (in Ref. 1);
Sequence-Conflict 360 -> 362
[Shao93a, UniProt10]
Alternate sequence: ASP → GNR; UniProt: (in Ref. 1);
Sequence-Conflict 372
[Shao93a, UniProt10]
Alternate sequence: A → G; UniProt: (in Ref. 1);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b2797 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11623; 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

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.

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

Newman80: 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

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220

Shao93a: Shao Z, Newman EB (1993). "Sequencing and characterization of the sdaB gene from Escherichia coli K-12." Eur J Biochem 1993;212(3);777-84. PMID: 8385012

Shao94: Shao Z, Lin RT, Newman EB (1994). "Sequencing and characterization of the sdaC gene and identification of the sdaCB operon in Escherichia coli K12." Eur J Biochem 1994;222(3);901-7. PMID: 8026499

Su91: Su H, Newman EB (1991). "A novel L-serine deaminase activity in Escherichia coli K-12." J Bacteriol 1991;173(8);2473-80. PMID: 2013569

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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."


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 Sun Nov 23, 2014, BIOCYC13B.