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Escherichia coli K-12 substr. MG1655 Enzyme: seryl-tRNA synthetase



Gene: serS Accession Numbers: EG10947 (EcoCyc), b0893, ECK0884

Regulation Summary Diagram: ?

Subunit composition of seryl-tRNA synthetase = [SerS]2
         seryl-tRNA synthetase = SerS

Summary:
Seryl-tRNA synthetase (SerRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. SerRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology [Eriani90a, Cusack91].

SerRS is a dimer in solution [Katze70].

Specificity determinants within tRNASer that are important for recognition by SerRS have been identified [Rogers88, Schatz91, Asahara93, Sampson93, Asahara94, Saks96]. SerRS also aminoacylates a special tRNA, tRNASec, with serine [Leinfelder88]. The charging efficiency for tRNASec is approximately 1% of that for tRNASer [Baron91]. The serine residue of Ser-tRNASec is subsequently converted to selenocysteine by selenocysteine synthase. tRNASec recognizes the stop codon UGA.

SerRS lacks an editing domain, but pre-transfer editing (hydrolysis) of non-cognate aminoacyl adenylate intermediates may proceed within the enzyme active site itself [GruicSovulj07].

The reaction mechanism of SerRS includes the formation of an aminoacyl adenylate intermediate, which then serves as the animo acid donor in the aminoacyl-tRNA synthetase reaction [Lagerkvist77]. The N-terminal coiled coil domain of SerRS is required for its aminoacylation activity, but is not required for amino acid activation [Borel94]. This domain is an autonomously folding unit [Oakley97]. The C-terminal domain contains the dimer interface and the active site [Cusack90]; the Glu355 residue is conserved and important for activity [Vincent95].

Crystal structures of SerRS in various conformations have been solved [Cusack90, Price93]; however, they have not been deposited in PDB.

Reviews: [Ibba00, Leberman91, Lenhard99]

Locations: cytosol

Map Position: [938,651 -> 939,943] (20.23 centisomes)
Length: 1293 bp / 430 aa

Molecular Weight of Polypeptide: 48.414 kD (from nucleotide sequence), 47 kD (experimental) [Katze70 ]

Molecular Weight of Multimer: 95 kD (experimental) [Katze70]

Unification Links: ASAP:ABE-0003038 , CGSC:169 , DIP:DIP-35989N , EchoBASE:EB0940 , EcoGene:EG10947 , EcoliWiki:b0893 , Mint:MINT-1230011 , ModBase:P0A8L1 , OU-Microarray:b0893 , PortEco:serS , PR:PRO_000023935 , Pride:P0A8L1 , Protein Model Portal:P0A8L1 , RefSeq:NP_415413 , RegulonDB:EG10947 , SMR:P0A8L1 , String:511145.b0893 , UniProt:P0A8L1

Relationship Links: InterPro:IN-FAMILY:IPR002314 , InterPro:IN-FAMILY:IPR002317 , InterPro:IN-FAMILY:IPR006195 , InterPro:IN-FAMILY:IPR010978 , InterPro:IN-FAMILY:IPR015866 , Panther:IN-FAMILY:PTHR11778 , Pfam:IN-FAMILY:PF00587 , Pfam:IN-FAMILY:PF02403 , Prints:IN-FAMILY:PR00981 , Prosite:IN-FAMILY:PS50862

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006434 - seryl-tRNA aminoacylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Vincent95, Katze70]
GO:0016260 - selenocysteine biosynthetic process Inferred from experiment Inferred by computational analysis [GOA06, Baron91]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01]
GO:0097056 - selenocysteinyl-tRNA(Sec) biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Airas07]
GO:0004828 - serine-tRNA ligase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Vincent95, Katze70]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Lasserre06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

MultiFun Terms: information transfer protein related amino acid -activation

Essentiality data for serS 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 ? 31-Dec-2012 by Keseler I , SRI International


Enzymatic reaction of: L-serine:tRNASer ligase (AMP-forming) (seryl-tRNA synthetase)

Synonyms: SerRS, seryl-tRNA synthetase

EC Number: 6.1.1.11

tRNAser + L-serine + ATP + H+ <=> L-seryl-tRNAser + AMP + diphosphate

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

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA charging

Summary:
The magnesium dependency of the equilibrium constant of SerRS has been measured [Airas07].

Cofactors or Prosthetic Groups: Mg2+ [Airas07, Katze70]

Inhibitors (Competitive): serine methyl ester [Ahel05] , serine hydroxamate [Tosa71, Ahel05] , serinamide [Ahel05]

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-serine
70.0
[Katze70]
ATP
0.068
[Borel94]
tRNAser
1.2
[Baron91]

pH(opt): 8.2-8.8 [Katze70]


Enzymatic reaction of: L-serine:tRNASec ligase (AMP-forming) (seryl-tRNA synthetase)

EC Number: 6.1.1.11

tRNAsec + L-serine + ATP + H+ <=> L-seryl-tRNAsec + AMP + diphosphate

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

The reaction is physiologically favored in the direction shown.

In Pathways: selenocysteine biosynthesis I (bacteria)

Kinetic Parameters:

Substrate
Km (μM)
Citations
tRNAsec
11.2
[Baron91]


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 237 -> 239
[UniProt10a]
UniProt: Serine binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 268 -> 270
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 291
[UniProt10a]
UniProt: Serine; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 355
[Vincent95, UniProt11]
Alternate sequence: E → Q; UniProt: Loss of serine activation activity.
Nucleotide-Phosphate-Binding-Region 355 -> 358
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 391
[UniProt10a]
UniProt: Serine; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0893 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10947; confirmed by SwissProt match.


References

Ahel05: Ahel D, Slade D, Mocibob M, Soll D, Weygand-Durasevic I (2005). "Selective inhibition of divergent seryl-tRNA synthetases by serine analogues." FEBS Lett 579(20);4344-8. PMID: 16054140

Airas07: Airas RK (2007). "Magnesium dependence of the measured equilibrium constants of aminoacyl-tRNA synthetases." Biophys Chem 131(1-3);29-35. PMID: 17889423

Asahara93: Asahara H, Himeno H, Tamura K, Nameki N, Hasegawa T, Shimizu M (1993). "Discrimination among E. coli tRNAs with a long variable arm." Nucleic Acids Symp Ser (29);207-8. PMID: 7504246

Asahara94: Asahara H, Himeno H, Tamura K, Nameki N, Hasegawa T, Shimizu M (1994). "Escherichia coli seryl-tRNA synthetase recognizes tRNA(Ser) by its characteristic tertiary structure." J Mol Biol 236(3);738-48. PMID: 8114091

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

Baron90: Baron C, Heider J, Bock A (1990). "Mutagenesis of selC, the gene for the selenocysteine-inserting tRNA-species in E. coli: effects on in vivo function." Nucleic Acids Res 18(23);6761-6. PMID: 1702199

Baron91: Baron C, Bock A (1991). "The length of the aminoacyl-acceptor stem of the selenocysteine-specific tRNA(Sec) of Escherichia coli is the determinant for binding to elongation factors SELB or Tu." J Biol Chem 266(30);20375-9. PMID: 1939093

Borel94: Borel F, Vincent C, Leberman R, Hartlein M (1994). "Seryl-tRNA synthetase from Escherichia coli: implication of its N-terminal domain in aminoacylation activity and specificity." Nucleic Acids Res 22(15);2963-9. PMID: 8065908

Cusack90: Cusack S, Berthet-Colominas C, Hartlein M, Nassar N, Leberman R (1990). "A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A." Nature 347(6290);249-55. PMID: 2205803

Cusack91: Cusack S, Hartlein M, Leberman R (1991). "Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases." Nucleic Acids Res 19(13);3489-98. PMID: 1852601

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

Eriani90a: Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990). "Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs." Nature 347(6289);203-6. PMID: 2203971

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.

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

GruicSovulj07: Gruic-Sovulj I, Rokov-Plavec J, Weygand-Durasevic I (2007). "Hydrolysis of non-cognate aminoacyl-adenylates by a class II aminoacyl-tRNA synthetase lacking an editing domain." FEBS Lett 581(26);5110-4. PMID: 17931630

Ibba00: Ibba M, Soll D (2000). "Aminoacyl-tRNA synthesis." Annu Rev Biochem 69;617-50. PMID: 10966471

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

Katze70: Katze JR, Konigsberg W (1970). "Purification and properties of seryl transfer ribonucleic acid synthetase from Escherichia coli." J Biol Chem 245(5);923-30. PMID: 4906848

Lagerkvist77: Lagerkvist U, Akesson B, Branden R (1977). "Aminoacyl adenylate, a normal intermediate or a dead end in aminoacylation of transfer ribonucleic acid." J Biol Chem 252(3);1002-6. PMID: 320199

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Leberman91: Leberman R, Hartlein M, Cusack S (1991). "Escherichia coli seryl-tRNA synthetase: the structure of a class 2 aminoacyl-tRNA synthetase." Biochim Biophys Acta 1089(3);287-98. PMID: 1859832

Leinfelder88: Leinfelder W, Zehelein E, Mandrand-Berthelot MA, Bock A (1988). "Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine." Nature 331(6158);723-5. PMID: 2963963

Lenhard99: Lenhard B, Orellana O, Ibba M, Weygand-Durasevic I (1999). "tRNA recognition and evolution of determinants in seryl-tRNA synthesis." Nucleic Acids Res 27(3);721-9. PMID: 9889265

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

Low71: Low B, Gates F, Goldstein T, Soll D (1971). "Isolation and partial characterization of temperature-sensitive Escherichia coli mutants with altered leucyl- and seryl-transfer ribonucleic acid synthetases." J Bacteriol 108(2);742-50. PMID: 4942762

Oakley97: Oakley MG, Kim PS (1997). "Protein dissection of the antiparallel coiled coil from Escherichia coli seryl tRNA synthetase." Biochemistry 36(9);2544-9. PMID: 9054560

Price93: Price S, Cusack S, Borel F, Berthet-Colominas C, Leberman R (1993). "Crystallization of the seryl-tRNA synthetase:tRNAS(ser) complex of Escherichia coli." FEBS Lett 324(2);167-70. PMID: 8508916

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

Rogers88: Rogers MJ, Soll D (1988). "Discrimination between glutaminyl-tRNA synthetase and seryl-tRNA synthetase involves nucleotides in the acceptor helix of tRNA." Proc Natl Acad Sci U S A 85(18);6627-31. PMID: 3045821

Saks96: Saks ME, Sampson JR (1996). "Variant minihelix RNAs reveal sequence-specific recognition of the helical tRNA(Ser) acceptor stem by E.coli seryl-tRNA synthetase." EMBO J 15(11);2843-9. PMID: 8654382

Sampson93: Sampson JR, Saks ME (1993). "Contributions of discrete tRNA(Ser) domains to aminoacylation by E.coli seryl-tRNA synthetase: a kinetic analysis using model RNA substrates." Nucleic Acids Res 21(19);4467-75. PMID: 8233780

Schatz91: Schatz D, Leberman R, Eckstein F (1991). "Interaction of Escherichia coli tRNA(Ser) with its cognate aminoacyl-tRNA synthetase as determined by footprinting with phosphorothioate-containing tRNA transcripts." Proc Natl Acad Sci U S A 88(14);6132-6. PMID: 2068094

Tosa71: Tosa T, Pizer LI (1971). "Biochemical bases for the antimetabolite action of L-serine hydroxamate." J Bacteriol 106(3);972-82. PMID: 4934072

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

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

Vincent95: Vincent C, Borel F, Willison JC, Leberman R, Hartlein M (1995). "Seryl-tRNA synthetase from Escherichia coli: functional evidence for cross-dimer tRNA binding during aminoacylation." Nucleic Acids Res 23(7);1113-8. PMID: 7537870

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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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 Mon Dec 22, 2014, biocyc13.