Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015

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

Gene: cysS Accession Numbers: EG10196 (EcoCyc), b0526, ECK0519

Synonyms: syc

Regulation Summary Diagram: ?

Regulation summary diagram for cysS

Cysteinyl-tRNA synthetase (CysRS) 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. CysRS belongs to the Class I aminoacyl tRNA synthetases [Eriani90, Landes95].

CysRS is a monomer in solution [Eriani91]. The N-terminal domain of CysRS is active in adenylate synthesis, while the C-terminal domain is able to bind and discriminate tRNA. The two domains can not complement each other in trans, showing that full enzymatic activity requires covalent continuity [Zhang05]. Molecular dynamics analysis of the enzyme has allowed identification of key residues involved in communication between the two domains, and kinetic analysis of mutant enzymes confirmed their importance [Ghosh11].

Specificity determinants within tRNACys that are important for recognition by CysRS have been identified [Pallanck92, Hou93, Komatsoulis93, Hou95, Hou95a, Christian00, Hou01]. Specificity determinants and residues within CysRS that are important for catalytic activity have been investigated [Ohannesian96]. Recognition of the 1-72 base pair of the tRNA acceptor end is accomplished by an α-helical motif insertion in the Rossmann-fold domain of CysRS [Liu11].

A crystal structure of CysRS bound to tRNACys was determined at 2.3 Å resolution, showing extensive base-selective and shape-specific RNA-protein interactions [Hauenstein04]. The efficiency of CysRS aminoacylation is modulated by the G15-G48 Levitt pair together with tertiary nucleotides surrounding it in tRNACys [Sherlin00].

Investigation of pre-steady-state and single turnover kinetics of CysRS show that the enzyme exhibits burst kinetics and is rate-limited by release of aminoacyl-tRNA, distinguishing it from class II aminoacyl tRNA synthetases [Zhang06].

Unlike other aminoacyl-tRNA synthetases, CysRS does not possess an editing mechanism to discriminate against non-cognate amino acids [Fersht79]. Crystal structures of CysRS in the apo- and cysteine-bound state have been determined at 2.3 and 2.6 Å resolution, revealing a zinc ion at the base of the active site cleft [Newberry02]. The zinc ion is responsible for the ability of CysRS to bind cysteine specifically, although CysRS does not possess amino acid editing activity [Zhang03, Zhang03a].

Unlike other class I aminoacyl-tRNA synthetases, CysRS is able to attach cysteine to both the 2' and 3' hydroxyl groups of A76 in tRNACys. However, aminoacylation of the 3' hydroxyl group has a 20-fold lower kcat/Km than that of the 2' hydroxyl group. The conserved nucleotide U73 in tRNACys appears to confer this flexibility [Shitivelband05].

Review: [Ibba00]

Citations: [Zhang08]

Locations: cytosol

Map Position: [553,834 -> 555,219] (11.94 centisomes, 43°)
Length: 1386 bp / 461 aa

Molecular Weight of Polypeptide: 52.202 kD (from nucleotide sequence), 55 kD (experimental) [Hou91 ]

Unification Links: ASAP:ABE-0001810 , CGSC:888 , DIP:DIP-9386N , EchoBASE:EB0193 , EcoGene:EG10196 , EcoliWiki:b0526 , Mint:MINT-1240309 , ModBase:P21888 , OU-Microarray:b0526 , PortEco:cysS , PR:PRO_000022387 , Pride:P21888 , Protein Model Portal:P21888 , RefSeq:NP_415059 , RegulonDB:EG10196 , SMR:P21888 , String:511145.b0526 , UniProt:P21888

Relationship Links: InterPro:IN-FAMILY:IPR009080 , InterPro:IN-FAMILY:IPR014729 , InterPro:IN-FAMILY:IPR015273 , InterPro:IN-FAMILY:IPR015803 , InterPro:IN-FAMILY:IPR024909 , Panther:IN-FAMILY:PTHR10890 , PDB:Structure:1LI5 , PDB:Structure:1LI7 , PDB:Structure:1U0B , Pfam:IN-FAMILY:PF01406 , Pfam:IN-FAMILY:PF09190 , Prints:IN-FAMILY:PR00983 , Prosite:IN-FAMILY:PS00178 , Smart:IN-FAMILY:SM00840

In Paralogous Gene Group: 150 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006423 - cysteinyl-tRNA aminoacylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Zhang03]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11a]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01a]
Molecular Function: GO:0004812 - aminoacyl-tRNA ligase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Zhang03]
GO:0004817 - cysteine-tRNA ligase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Zhang03]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Newberry02]
GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA06, Newberry02, Zhang03]
GO:0016874 - ligase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Zhang03]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Zhang03]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Gaudet10]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: information transfer protein related amino acid -activation

Essentiality data for cysS knockouts: ?

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

Last-Curated ? 23-Dec-2011 by Keseler I , SRI International

Enzymatic reaction of: cysteinyl-tRNA synthetase

Synonyms: CysRS

EC Number:

a tRNAcys + L-cysteine + ATP + H+ <=> an L-cysteinyl-[tRNAcys] + AMP + diphosphate

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 physiologically favored in the direction shown.

In Pathways: tRNA charging

Cofactors or Prosthetic Groups: Zn2+ [Newberry02]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Ruan04, BRENDA14]
29.0, 31.0, 22.0
35.0, 79.0, 100.0
1.21, 2.72, 3.45, 1.13, 2.55, 3.23, 1.59, 3.59, 4.55
[Zhang03, BRENDA14]
[Ruan04, BRENDA14]
[Zhang05, BRENDA14]
220.0, 290.0
57.0, 91.0, 142.0
0.26, 0.41, 0.65, 0.2, 0.31, 0.49
[Zhang03, BRENDA14]
a tRNAcys
[Ruan04, BRENDA14]
a tRNAcys
[Hauenstein04, BRENDA14]
a tRNAcys
0.4, 1.2, 0.35
0.5, 0.9, 2.5
1.25, 2.25, 6.25, 0.42, 0.75, 2.08, 1.43, 2.57, 7.14
[Zhang03, BRENDA14]
a tRNAcys
[Zhang06, BRENDA14]
a tRNAcys
3.0, 3.47
2.0, 2.31
[Sherlin00, BRENDA14]

Sequence Features

Protein sequence of cysteinyl-tRNA synthetase with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 28
UniProt: Zinc.
Protein-Segment 30 -> 40
UniProt: "HIGH" region; Sequence Annotation Type: short sequence motif.
Acetylation-Modification 73
Metal-Binding-Site 209
UniProt: Zinc.
Metal-Binding-Site 234
UniProt: Zinc.
Metal-Binding-Site 238
UniProt: Zinc.
Protein-Segment 266 -> 270
UniProt: "KMSKS" region; Sequence Annotation Type: short sequence motif.
Amino-Acid-Sites-That-Bind 269
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 316
[Eriani91, UniProt10a]
UniProt: (in Ref. 1; CAA39691);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b0526 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10196; confirmed by SwissProt match.


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."

Christian00: Christian T, Lipman RS, Evilia C, Hou YM (2000). "Alternative design of a tRNA core for aminoacylation." J Mol Biol 303(4);503-14. PMID: 11054287

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

Eriani90: 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

Eriani91: Eriani G, Dirheimer G, Gangloff J (1991). "Cysteinyl-tRNA synthetase: determination of the last E. coli aminoacyl-tRNA synthetase primary structure." Nucleic Acids Res 19(2);265-9. PMID: 2014166

Fersht79: Fersht AR, Dingwall C (1979). "Cysteinyl-tRNA synthetase from Escherichia coli does not need an editing mechanism to reject serine and alanine. High binding energy of small groups in specific molecular interactions." Biochemistry 18(7);1245-9. PMID: 371674

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Ghosh11: Ghosh A, Sakaguchi R, Liu C, Vishveshwara S, Hou YM (2011). "Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout." J Biol Chem 286(43);37721-31. PMID: 21890630

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."

Hauenstein04: Hauenstein S, Zhang CM, Hou YM, Perona JJ (2004). "Shape-selective RNA recognition by cysteinyl-tRNA synthetase." Nat Struct Mol Biol 11(11);1134-41. PMID: 15489861

Hou01: Hou YM, Zhang X, Holland JA, Davis DR (2001). "An important 2'-OH group for an RNA-protein interaction." Nucleic Acids Res 29(4);976-85. PMID: 11160931

Hou91: Hou YM, Shiba K, Mottes C, Schimmel P (1991). "Sequence determination and modeling of structural motifs for the smallest monomeric aminoacyl-tRNA synthetase." Proc Natl Acad Sci U S A 88(3);976-80. PMID: 1992490

Hou93: Hou YM, Westhof E, Giege R (1993). "An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA." Proc Natl Acad Sci U S A 90(14);6776-80. PMID: 8341698

Hou95: Hou YM (1995). "RNA recognition based on a pair of tertiary hydrogen interaction." Nucleic Acids Symp Ser (33);172-5. PMID: 8643362

Hou95a: Hou YM, Sterner T, Bhalla R (1995). "Evidence for a conserved relationship between an acceptor stem and a tRNA for aminoacylation." RNA 1(7);707-13. PMID: 7585255

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

Komatsoulis93: Komatsoulis GA, Abelson J (1993). "Recognition of tRNA(Cys) by Escherichia coli cysteinyl-tRNA synthetase." Biochemistry 32(29);7435-44. PMID: 8338841

Landes95: Landes C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL (1995). "A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases." Biochimie 77(3);194-203. PMID: 7647112

Liu11: Liu C, Sanders JM, Pascal JM, Hou YM (2011). "Adaptation to tRNA acceptor stem structure by flexible adjustment in the catalytic domain of class I tRNA synthetases." RNA. PMID: 22184460

Newberry02: Newberry KJ, Hou YM, Perona JJ (2002). "Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase." EMBO J 21(11);2778-87. PMID: 12032090

Ohannesian96: Ohannesian DW, Oh J, Hou YM (1996). "Mutational analysis of a leucine heptad repeat motif in a class I aminoacyl-tRNA synthetase." Biochemistry 35(45);14405-12. PMID: 8916927

Pallanck92: Pallanck L, Li S, Schulman LH (1992). "The anticodon and discriminator base are major determinants of cysteine tRNA identity in vivo." J Biol Chem 267(11);7221-3. PMID: 1373131

Ruan04: Ruan B, Nakano H, Tanaka M, Mills JA, DeVito JA, Min B, Low KB, Battista JR, Soll D (2004). "Cysteinyl-tRNA(Cys) formation in Methanocaldococcus jannaschii: the mechanism is still unknown." J Bacteriol 186(1);8-14. PMID: 14679218

Sherlin00: Sherlin LD, Bullock TL, Newberry KJ, Lipman RS, Hou YM, Beijer B, Sproat BS, Perona JJ (2000). "Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases." J Mol Biol 299(2);431-46. PMID: 10860750

Shitivelband05: Shitivelband S, Hou YM (2005). "Breaking the stereo barrier of amino acid attachment to tRNA by a single nucleotide." J Mol Biol 348(3);513-21. PMID: 15826650

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

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

Zhang03: Zhang CM, Christian T, Newberry KJ, Perona JJ, Hou YM (2003). "Zinc-mediated amino acid discrimination in cysteinyl-tRNA synthetase." J Mol Biol 327(5);911-7. PMID: 12662918

Zhang03a: Zhang CM, Perona JJ, Hou YM (2003). "Amino acid discrimination by a highly differentiated metal center of an aminoacyl-tRNA synthetase." Biochemistry 42(37);10931-7. PMID: 12974627

Zhang05: Zhang CM, Hou YM (2005). "Domain-domain communication for tRNA aminoacylation: the importance of covalent connectivity." Biochemistry 44(19);7240-9. PMID: 15882062

Zhang06: Zhang CM, Perona JJ, Ryu K, Francklyn C, Hou YM (2006). "Distinct kinetic mechanisms of the two classes of Aminoacyl-tRNA synthetases." J Mol Biol 361(2);300-11. PMID: 16843487

Zhang08: Zhang CM, Liu C, Christian T, Gamper H, Rozenski J, Pan D, Randolph JB, Wickstrom E, Cooperman BS, Hou YM (2008). "Pyrrolo-C as a molecular probe for monitoring conformations of the tRNA 3' end." RNA 14(10);2245-53. PMID: 18755841

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 19.0 on Sun Aug 30, 2015, biocyc13.