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

Gene: hisS Accession Numbers: EG10453 (EcoCyc), b2514, ECK2510

Regulation Summary Diagram: ?

Regulation summary diagram for hisS

Subunit composition of histidyl-tRNA synthetase = [HisS]2
         histidyl-tRNA synthetase = HisS

Histidyl-tRNA synthetase (HisRS) 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. HisRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology [Eriani90, Cusack91].

HisRS is a dimer in solution [Kalousek74]. The C-terminal domain of the protein is required for dimerization, while the N-terminal domain contains most of the catalytic activity. The two domains do not complement each other in trans [Augustine97]. Minimal active site fragments likely representing the ancestral "urzyme" have been studied [Li11e].

Specificity determinants within tRNAHis that are important for recognition by HisRS have been identified; the unique G-1:C73 base pair was found to play a crucial role [Himeno89, Yan94, Fromant00, Rosen04a, Guth07]. Specificity determinants and residues within HisRS that are important for catalytic activity have been investigated [Yan95, Ruhlmann97, Bovee99, Hawko01, Connolly04, Guth07], and a model for the catalytic cycle was proposed [Guth07]. The C-terminal domain of HisRS was found to be largely responsible for recognition of the tRNAHis anticodon [Yan96].

Crystal structures of HisRS have been determined, and a reaction mechanism was proposed [Arnez95, Arnez97]. Various types of experiments support a substrate-assisted concerted reaction mechanism [Guth05]. Catalysis may occur at sites alternating between the two monomers; conformational changes may be rate-limiting for product formation [Guth07, Guth09]. The mechanisms of substrate discrimination [Banik09, Banik10] and the aminoacylation reaction [Banik11] have been modeled.

Reviews: [Freist99, Ibba00]

Gene Citations: [Freedman85]

Locations: cytosol

Map Position: [2,637,323 <- 2,638,597] (56.84 centisomes, 205°)
Length: 1275 bp / 424 aa

Molecular Weight of Polypeptide: 47.029 kD (from nucleotide sequence), 42 kD (experimental) [Kalousek74 ]

Molecular Weight of Multimer: 86 kD (experimental) [Kalousek74]

Unification Links: ASAP:ABE-0008278 , CGSC:624 , DIP:DIP-35894N , EchoBASE:EB0448 , EcoGene:EG10453 , EcoliWiki:b2514 , Mint:MINT-1236095 , ModBase:P60906 , OU-Microarray:b2514 , PortEco:hisS , PR:PRO_000022903 , Pride:P60906 , Protein Model Portal:P60906 , RefSeq:NP_417009 , RegulonDB:EG10453 , SMR:P60906 , String:511145.b2514 , UniProt:P60906

Relationship Links: InterPro:IN-FAMILY:IPR002314 , InterPro:IN-FAMILY:IPR004154 , InterPro:IN-FAMILY:IPR004516 , InterPro:IN-FAMILY:IPR006195 , InterPro:IN-FAMILY:IPR015807 , Panther:IN-FAMILY:PTHR11476 , PDB:Structure:1HTT , PDB:Structure:1KMM , PDB:Structure:1KMN , PDB:Structure:2EL9 , Pfam:IN-FAMILY:PF00587 , Pfam:IN-FAMILY:PF03129 , Prosite:IN-FAMILY:PS50862

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006427 - histidyl-tRNA aminoacylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Kalousek74]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11a]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01a]
Molecular Function: GO:0004821 - histidine-tRNA ligase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Kalousek74]
GO:0042803 - protein homodimerization activity Inferred from experiment [Kalousek74]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: information transfer protein related amino acid -activation

Essentiality data for hisS knockouts: ?

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

Last-Curated ? 08-Sep-2011 by Keseler I , SRI International

Enzymatic reaction of: histidyl-tRNA synthetase

Synonyms: HisRS

EC Number:

a tRNAhis + L-histidine + ATP + H+ <=> an L-histidyl-[tRNAhis] + 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: Mg2+ [Airas96]

Inhibitors (Competitive): histidinol [Kalousek74]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Rosen06, BRENDA14]
[Ruhlmann97, BRENDA14]
740.0, 890.0
0.17, 120.0
2.3e-4, 0.16, 1.9e-4, 0.13
[Augustine97, BRENDA14]
a tRNAhis
0.56, 1.4
[Augustine97, BRENDA14]
a tRNAhis
a tRNAhis
[Rosen06, BRENDA14]
a tRNAhis
[Guth05, BRENDA14]
6.0, 7.0
0.75, 0.88
[Ruhlmann97, BRENDA14]
46.0, 30.0
0.19, 142.0
0.0041, 3.09, 0.0063, 4.73
[Augustine97, BRENDA14]
[Rosen06, BRENDA14]

pH(opt): 8 [BRENDA14, Kalousek74], 7.4 [Kalousek74]

Sequence Features

Protein sequence of histidyl-tRNA synthetase with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
UniProt: Removed.
Chain 2 -> 424
UniProt: Histidyl-tRNA synthetase;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2514 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10453; confirmed by SwissProt match.


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

Airas96: Airas RK (1996). "Differences in the magnesium dependences of the class I and class II aminoacyl-tRNA synthetases from Escherichia coli." Eur J Biochem 240(1);223-31. PMID: 8797857

Arnez95: Arnez JG, Harris DC, Mitschler A, Rees B, Francklyn CS, Moras D (1995). "Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate." EMBO J 14(17);4143-55. PMID: 7556055

Arnez97: Arnez JG, Augustine JG, Moras D, Francklyn CS (1997). "The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase." Proc Natl Acad Sci U S A 94(14);7144-9. PMID: 9207058

Augustine97: Augustine J, Francklyn C (1997). "Design of an active fragment of a class II aminoacyl-tRNA synthetase and its significance for synthetase evolution." Biochemistry 36(12);3473-82. PMID: 9131996

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

Banik09: Banik SD, Nandi N (2009). "Orientation and distance dependent chiral discrimination in the first step of the aminoacylation reaction: integrated molecular orbital and semi-empirical method (ONIOM) based calculation." Colloids Surf B Biointerfaces 74(2);468-76. PMID: 19682871

Banik10: Banik SD, Nandi N (2010). "Aminoacylation reaction in the histidyl-tRNA synthetase: fidelity mechanism of the activation step." J Phys Chem B 114(6);2301-11. PMID: 20104869

Banik11: Banik SD, Nandi N (2011). "Influence of the conserved active site residues of histidyl tRNA synthetase on the mechanism of aminoacylation reaction." Biophys Chem 158(1);61-72. PMID: 21636210

Bovee99: Bovee ML, Yan W, Sproat BS, Francklyn CS (1999). "tRNA discrimination at the binding step by a class II aminoacyl-tRNA synthetase." Biochemistry 38(41);13725-35. PMID: 10521280

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Connolly04: Connolly SA, Rosen AE, Musier-Forsyth K, Francklyn CS (2004). "G-1:C73 recognition by an arginine cluster in the active site of Escherichia coli histidyl-tRNA synthetase." Biochemistry 43(4);962-9. PMID: 14744140

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

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

Freedman85: Freedman R, Gibson B, Donovan D, Biemann K, Eisenbeis S, Parker J, Schimmel P (1985). "Primary structure of histidine-tRNA synthetase and characterization of hisS transcripts." J Biol Chem 1985;260(18);10063-8. PMID: 2991272

Freist99: Freist W, Verhey JF, Ruhlmann A, Gauss DH, Arnez JG (1999). "Histidyl-tRNA synthetase." Biol Chem 380(6);623-46. PMID: 10430027

Fromant00: Fromant M, Plateau P, Blanquet S (2000). "Function of the extra 5'-phosphate carried by histidine tRNA." Biochemistry 39(14);4062-7. PMID: 10747795

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."

Guth05: Guth E, Connolly SH, Bovee M, Francklyn CS (2005). "A substrate-assisted concerted mechanism for aminoacylation by a class II aminoacyl-tRNA synthetase." Biochemistry 44(10);3785-94. PMID: 15751955

Guth07: Guth EC, Francklyn CS (2007). "Kinetic discrimination of tRNA identity by the conserved motif 2 loop of a class II aminoacyl-tRNA synthetase." Mol Cell 25(4);531-42. PMID: 17317626

Guth09: Guth E, Farris M, Bovee M, Francklyn CS (2009). "Asymmetric amino acid activation by class II histidyl-tRNA synthetase from Escherichia coli." J Biol Chem 284(31);20753-62. PMID: 19487703

Hawko01: Hawko SA, Francklyn CS (2001). "Covariation of a specificity-determining structural motif in an aminoacyl-tRNA synthetase and a tRNA identity element." Biochemistry 40(7);1930-6. PMID: 11329259

Himeno89: Himeno H, Hasegawa T, Ueda T, Watanabe K, Miura K, Shimizu M (1989). "Role of the extra G-C pair at the end of the acceptor stem of tRNA(His) in aminoacylation." Nucleic Acids Res 17(19);7855-63. PMID: 2678006

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

Kalousek74: Kalousek F, Konigsberg WH (1974). "Purification and characterization of histidyl transfer ribonucleic acid synthetase of Escherichia coli." Biochemistry 13(5);999-1006. PMID: 4591623

Li11e: Li L, Weinreb V, Francklyn C, Carter CW (2011). "Histidyl-tRNA synthetase urzymes: Class I and II aminoacyl tRNA synthetase urzymes have comparable catalytic activities for cognate amino acid activation." J Biol Chem 286(12);10387-95. PMID: 21270472

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

Rosen04a: Rosen AE, Musier-Forsyth K (2004). "Recognition of G-1:C73 atomic groups by Escherichia coli histidyl-tRNA synthetase." J Am Chem Soc 126(1);64-5. PMID: 14709061

Rosen06: Rosen AE, Brooks BS, Guth E, Francklyn CS, Musier-Forsyth K (2006). "Evolutionary conservation of a functionally important backbone phosphate group critical for aminoacylation of histidine tRNAs." RNA 12(7);1315-22. PMID: 16741232

Ruhlmann97: Ruhlmann A, Cramer F, Englisch U (1997). "Isolation and analysis of mutated histidyl-tRNA synthetases from Escherichia coli." Biochem Biophys Res Commun 237(1);192-201. PMID: 9266856

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 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."

Yan94: Yan W, Francklyn C (1994). "Cytosine 73 is a discriminator nucleotide in vivo for histidyl-tRNA in Escherichia coli." J Biol Chem 269(13);10022-7. PMID: 8144499

Yan95: Yan W, Francklyn C (1995). "tRNA selection by a class II aminoacyl-tRNA synthetase: the role of accessory domains and inter-domain communication in RNA recognition." Nucleic Acids Symp Ser (33);167-9. PMID: 8643360

Yan96: Yan W, Augustine J, Francklyn C (1996). "A tRNA identity switch mediated by the binding interaction between a tRNA anticodon and the accessory domain of a class II aminoacyl-tRNA synthetase." Biochemistry 35(21);6559-68. PMID: 8639604

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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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