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Histidyl-tRNA Synthetase

Histidyl tRNA Synthetase (HisRS) is a 94kD that belongs to the class II of aminoacyl-tRNA synthetases (aaRS). Aminoacyl-tRNA synthetases Aminoacyl-tRNA synthetases have been partitioned into two classes, containing 10 members, on the basis of sequence comparisons^[1]. Class I and Class II differ mainly with respect to the topology of the catalytic fold and site of esterification on cognate tRNA^[1]. Class II enzymes have a composed of anti-parallel β-sheets and α-helices (residues 1-325). Additionally, class II enzymes can be further divided into three subgroups: class IIa, distinguished by an N-terminal catalytic domain and C-terminal accessory domain (later shown to be anticodon binding domain); class IIb, whose anticodon binding domain is located on the N-terminal side of the fold; and class IIc, encompassing the tetrameric PheRS and GlyRS class II synthetases.^[2]

spinqualitylabelsall models Structure of Histidyl-tRNA Synthetase (PDB entry 1KMM) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Class II aminoacyl-tRNA synthetases aminoacylate the 3'OH of their cognate tRNAs. Histidine Binding Pocket The active site to HisRS contains a histidine binding pocket composed of highly conserved residues found in distinct sequences motifs. First, the LV/AAGGGLDYY loop (or ) forms one wall of the binding pocket. This HisA loop is highly conserved and extends over a part of the active site[3]. Second, the glycine-rich β-strand (sequence AGGRYDGL preceding ) comprises the histidine binding pocket floor and wall. Finally, conserved side chains that make direct contact with histidine are Glu83 and Gly127 (), which contact the α-amino and α-carbonyl functional groups, respectively, and Glu131 (motif II) and Tyr264, which make hydrogen bonds to the Nδ and Nε, respectively, of the imidazole ring[3]. Adenosine Triphosphate Binding Many interactions are required to prepare ATP for attack by a bound histidine molecule and encourage the magnesium pyrophosphate moiety to act as a leaving group. Residues in the β strands and the loop portion of motif 2 are important in ATP contacts for HisRS[4]. Generally, residues involved in ATP binding are among the most highly conserved in the HisRS family and for the most part shared by all members in class II. The π-stacking interaction between the adenine ring of ATP and Phe125 provides specificity in the binding of ATP. The recognition of the N6 amino group of ATP involves the main chain carbonyl of Tyr122. The ATP ribose 2’ OH forms an additional contact with HisRS by hydrogen bonding with the main chain carbonyl of Thr281. Furthermore, conserved residues Arg113 and Glu115 stabilize the triphosphate group of ATP in a position such that it points back towards the adenine base. This conformation of ATP is evidently unique to class II aaRS[5]. The α phosphate of ATP interacts with conserved residue Arg113. The β and γ phosphates are neutralized by two coordinated magnesium ions that are positioned by water molecules and conserved Glu115[3]. Also, the γ phosphate forms additional interactions with conserved Arg121 and Arg311.

Mechanism

Electrophilic Catalysis

The HisRS active site contains a highly conserved residue, Arg259, takes part in electrophilic catalysis for the adenylation reaction. First, as Arg259 is positioned on the HisA loop serves to fix the α-carboxylate group of the histidine substrate as the attacking nucleophile^[6]. Second, the guanidinium group of Arg259 is positioned approximately 3 Å from the α-phosphate of ATP where it serves as the electrophilic catalyst. Arg113 as well as Arg259 are arranged to interact with α-phosphate of ATP and thereby stabilize negative charge developed on the non-bridging oxygens during the transition state aarsbk. Evidence for Arg259 playing a critical role in catalysis is observed in a two or three log decrease in activity when substituted with a histidine ^[4] or other amino acids^[7]. Arg259 also interacts with the phenolic OH of Tyr264, which in turn donates a hydrogen bond to the Nδ of the histidine substrate^[3]. Utilizing Arg259 for catalysis is unique to HisRS as other class II aaRS enzymes, AspRS^[8] and SerRS^[9], which use a divalent magnesium metal ion to coordinate the α-phosphate of ATP and serve as an electrophilic catalysis.

tRNA

Evolutionary Conservation

Structural Homology

3D Structures of Histidyl-tRNA Synthetase

Bacteria

1KMN

1KMM

1HTT

2EL9

Eukaryota

3LCO

3HRK

Archara

1WU7

References

1. ↑ ^{1.0 1.1} Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PMID:2203971 doi:http://dx.doi.org/10.1038/347203a0
2. ↑ Cusack S, Hartlein M, Leberman R. Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. Nucleic Acids Res. 1991 Jul 11;19(13):3489-98. PMID:1852601
3. ↑ ^{3.0 3.1 3.2 3.3} Francklyn, C., and Arnez, J.G. (2004) in Aminoacyl-tRNA Synthetases (Ibba, M.,Francklyn, C.,Cusack, S.. Eds.) Landes Publishing, Austin, TX
4. ↑ ^{4.0 4.1} Arnez JG, Augustine JG, Moras D, Francklyn CS. The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7144-9. PMID:9207058
5. ↑ Arnez JG, Moras D. Structural and functional considerations of the aminoacylation reaction. Trends Biochem Sci. 1997 Jun;22(6):211-6. PMID:9204708
6. ↑ Arnez JG, Flanagan K, Moras D, Simonson T. Engineering an Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments. Proteins. 1998 Aug 15;32(3):362-80. PMID:9715912
7. ↑ Ruhlmann A, Cramer F, Englisch U. Isolation and analysis of mutated histidyl-tRNA synthetases from Escherichia coli. Biochem Biophys Res Commun. 1997 Aug 8;237(1):192-201. PMID:9266856 doi:10.1006/bbrc.1997.7108
8. ↑ Poterszman A, Delarue M, Thierry JC, Moras D. Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase. J Mol Biol. 1994 Nov 25;244(2):158-67. PMID:7966328 doi:http://dx.doi.org/10.1006/jmbi.1994.1716
9. ↑ Belrhali H, Yaremchuk A, Tukalo M, Berthet-Colominas C, Rasmussen B, Bosecke P, Diat O, Cusack S. The structural basis for seryl-adenylate and Ap4A synthesis by seryl-tRNA synthetase. Structure. 1995 Apr 15;3(4):341-52. PMID:7613865