PDBsum entry 2nx8

Hydrolase

PDB id: 2nx8

Contents

Protein chain

168 a.a. *

Ligands

PO4

Metals

_ZN

Waters ×138

* Residue conservation analysis

PDB id:

2nx8

Name:

Hydrolase

Title:

The crystal structure of the tRNA-specific adenosine deaminase from streptococcus pyogenes

Structure:

tRNA-specific adenosine deaminase. Chain: a. Synonym: hypothetical protein m6_spy0214. Engineered: yes. Mutation: yes

Source:

Streptococcus pyogenes serotype m6. Organism_taxid: 301450. Strain: mgas10394. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.00Å R-factor: 0.214 R-free: 0.242

Authors:

K.Y.Hwang,W.-H.Lee,Y.K.Kim

Key ref:

W.H.Lee et al. (2007). Crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes. Proteins, 68, 1016-1019. PubMed id: 17554781 DOI: 10.1002/prot.21456

Date:

17-Nov-06 Release date: 21-Aug-07

Protein chain

Q5XE14  (TADA_STRP6) -  tRNA-specific adenosine deaminase from Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)

Seq: 171 a.a.

Struc: 168 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.4.33 - tRNA(adenine(34)) deaminase.
• Reaction: adenosine₃₄ in tRNA + H2O + H⁺ = inosine₃₄ in tRNA + NH4⁺
• Cofactor: Zn(2+)

DOI no: 10.1002/prot.21456

Proteins 68:1016-1019 (2007)

PubMed id: 17554781

Crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes.

W.H.Lee, Y.K.Kim, K.H.Nam, A.Priyadarshi, E.H.Lee, E.E.Kim, Y.H.Jeon, C.Cheong, K.Y.Hwang.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. (A) Overall structure A schematic ribbon diagram of the overall structure of the tRNA-specific adenosine deaminase (residues 5-173) from S. pyogenes (spTad A). The N- and C-termini of the protein are labeled, and the helices and sheets are numbered. Zn (II) and the phosphate ion are shown in gray sphere and ball-and-stick models, respectively. (B) Superimposition of spTadA and other proteins. The overall structure of spTadA is superimposed on other TadA proteins in a ribbon model representation. The blue, yellow, red and green colors are shown to S. pyogenes TadA, A. aeolicus TadA (1WWR), E. coli TadA (1Z3A), and Staphylococcus aureus TadA (2B3J), respectively. The red circles are shown in the main differences. (C) Comparison of active sites between spTadA and saTadA-complexed with RNA. A detailed depiction of the interacting residues of the active site compared to Staphylococcus aureus Tad A (saTadA) is shown by ball-and-stick models. In saTadA, the His residue has the - interaction with PURINE RIBOSIDE-5 -MONOPHOSPHATE (C[10] H[13] N[4] O[7] P) (PR5). Green residues are spTadA, yellow residues the saTad A (2B3J), blue the phosphate ion, PO[4]^- (spTad), and red is PR5 (2B3J). (D) The dimer interface of spTadA. The monomers interact with each other symmetrically. The residues participated in forming the interfaces are shown as ball-and-stick models and the interaction with another monomer. The hydrogen bonding and hydrophobic interactions are major forces in forming the dimer interface.

The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 68, 1016-1019) copyright 2007.