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 [Zhang05a]. 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, Christian00a, 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 [Liu11a].

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 [Zhang06a].

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 [Zhang03d, Zhang03e].

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: [Zhang08b]

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, GOA01, Zhang03d]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0004812 - aminoacyl-tRNA ligase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Zhang03d]
GO:0004817 - cysteine-tRNA ligase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Zhang03d]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Newberry02]
GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA06, Newberry02, Zhang03d]
GO:0016874 - ligase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, Zhang03d]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Zhang03d]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Gaudet10]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

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
[Zhang03d, BRENDA14]
[Ruan04, BRENDA14]
[Zhang05a, BRENDA14]
220.0, 290.0
57.0, 91.0, 142.0
0.26, 0.41, 0.65, 0.2, 0.31, 0.49
[Zhang03d, 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
[Zhang03d, BRENDA14]
a tRNAcys
[Zhang06a, 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."

Christian00a: 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, 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."

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

Liu11a: 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 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."

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

Zhang03d: 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

Zhang03e: 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

Zhang05a: Zhang CM, Hou YM (2005). "Domain-domain communication for tRNA aminoacylation: the importance of covalent connectivity." Biochemistry 44(19);7240-9. PMID: 15882062

Zhang06a: 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

Zhang08b: 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

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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