Database accession: MF7000976
Name: tRNA-specific adenosine deaminase (Streptococcus pyogenes)
PDB ID: 2nx8
Experimental method: X-ray (2.00 Å)
Assembly: Homodimer
Source organism: Streptococcus pyogenes serotype M6
Primary publication of the structure:
Lee WH, Kim YK, Nam KH, Priyadarshi A, Lee EH, Kim EE, Jeon YH, Cheong C, Hwang KY
Crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes.
(2007) Proteins 68: 1016-9
PMID: 17554781
Abstract:
Not available.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
cytosine deaminase activity cytosine deaminase activity
tRNA-specific adenosine-34 deaminase activity tRNA-specific adenosine-34 deaminase activity
zinc ion binding zinc ion binding
Biological process:
cytidine metabolic process cytidine metabolic process
cytosine metabolic process cytosine metabolic process
pyrimidine-containing compound salvage pyrimidine-containing compound salvage
tRNA wobble adenosine to inosine editing tRNA wobble adenosine to inosine editing
Cellular component:
cytoplasm cytoplasm
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: tRNA-specific adenosine deaminase
Source organism: Streptococcus pyogenes serotype M6
Length: 171 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMPYSLEEQTYFMQEALKEAEKSLQKAEIPIGCVIVKDGEIIGRGHNAREESNQAIMHAEMMAINEANAHEGNWRLLDTTLFVTIEPCVMCSGAIGLARIPHVIYGASNQKFGGADSLYQILTDERLNHRVQVERGLLAADCANIMQTFFRQGRERKKIAKHLIKEQSDPFD
UniProtKB AC: Q5XE14 (positions: 1-165)
Coverage: 96%
Name: tRNA-specific adenosine deaminase
Source organism: Streptococcus pyogenes serotype M6
Length: 171 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMPYSLEEQTYFMQEALKEAEKSLQKAEIPIGCVIVKDGEIIGRGHNAREESNQAIMHAEMMAINEANAHEGNWRLLDTTLFVTIEPCVMCSGAIGLARIPHVIYGASNQKFGGADSLYQILTDERLNHRVQVERGLLAADCANIMQTFFRQGRERKKIAKHLIKEQSDPFD
UniProtKB AC: Q5XE14 (positions: 1-165)
Coverage: 96%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: -
Evidence level: Insufficient evidence (candidate)
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The tRNA-specific adenosine deaminase, spTadA is a dimer in solution as demonstrated by gel-filtration. Dimer formation buries a large surface which is mainly formed by hydrophobic and nonpolar interactions. From the structural aspects, dimerization appears to be important for specific binding with tRNA and enzyme functions. The authors also suggest that because of the nonpolar interface, the formation of a dimer is energetically favorable compared with the monomer in solution. (PMID:17554781).
Chain A:
N/A
Chain A-2:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). No related structure was found in the MFIB database.
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