Download Field: CoA synthetase subunit alpha> cytoplasmic protein

Field: <succinyl-CoA synthetase subunit alpha> cytoplasmic protein
Author: Jia Yue Liu
Date: November 17, 2014
FACI_IFERC00001G1736
The BLASTp showed no conserved class of putative proteins was found. Peptide Statistics with
the Search Tool Uniprot showed similarity to the succinyl-CoA synthetase subunit alpha in
Picrophilus torridus, Thermoplasm volcanium, Archaeolobus fulgidus DSM 4304, Pseudomonas
aeruginosa PAO1.
Phylogenetic analysis showed the gene from F. acidarmanus Fer1 was clustering with
Thermoplasma and Picophilus. The next closest genes are those from Aciduliprofundum and
Methanohalophilus which are the next closest related genomes to the Ferroplasma genome, so
there is no evidence to suggest that this gene has recently undergone HGT.
SignalP predicted no Probable Signal Peptide found (p<0.450 and 0.570). Therefore no probable
cleavage site was predicted. TMHMM predicted no significant transmembrane helix.
Expected number of amino acids in TMHs is 220, which is more than 18 aa, indicating high
likelihood of protein being located as transmembrane or having a signal peptide. The expected
number of amino acids in transmembrane helices in the first 69 aa is 0.02374 aa, which is lower
than 10aa, indicating low likelihood of signal peptide at the N terminus. The N-terminus of the
protein is predicted (1) to be located extracellularly. The protein was predicted with 96%
confidence of being located extracellularly. However, given that no transmembrane helix was
predicted, this prediction is most likely not accurate.
Phobius also predicted an absence of a transmembrane helix, which indicates that the protein is
not directed to the membrane or extracellularly. Psortb and LipoP indicated that the protein is
located within the cytoplasm.
TIGRFAM and PDB both detected succinate-CoA ligase as their top hit. TIGRFAM further
elucidated that the HMM top hit from TIGRFAM describes succinate-CoA ligase as both ADPforming and GDP-forming.
Field: discussion
Author: genbank
Date: Wed Nov 05 17:12:01 UTC 2014
The cellular localization model of OID 638394059 is compliant with the cellular structure and
localization of the alpha-subunit of succinyl-CoA synthetase of ortholog from Sulfolobus
solfataricus, which forms an acid-labile phosphohistidyl enzyme intermediate during its catalytic
cycle [1].
The succinyl-CoA synthetase (EC 6.2.1.5) of Ferroplasma acidarmanus Fer1 is predicted to
catalyze the reversible reaction succinyl-CoA + NDP + Pi ↔ succinate + CoA + NTP (N
denoting adenosine or guanosine). The enzyme consists of two different subunits, designated α
and β.
From the data collected, succinyl-CoA synthetase possess a high content of basic, hydrophobic
and hydrophilic amino acids. Typically, cytoplasmic proteins possess a high levels of Arginine,
Histidine, Isoleucine, Glutamate and Methionine. In addition, there will be a larger proportion of
charged, aliphatic, hydrophilic residues. The results of the PEPSTAT predicted that the protein
contained 12.27 mol% of Isoleucine, 9.09 mol% of lysine and 4.09 mol% of leucine. There is a
low % (0.57%) of cysteine found which is indicative of a cytoplasmic protein.
Based on the results of the comparative databases involving cellular localization (PSORT-B,
Phobius, LipoP, TMHMM, SignalP), it is believed that the protein is located within the
cytoplasm. Hence, it is suggested to be an intracellular protein as previously postulated using the
PEPSTATS tool. While the TMHMM postulates that the protein is located extraceullarly, given
that no transmembrane helix was predicted, this prediction is most likely not accurate. Based on
the results from TMHMM and Phobius, the protein does not contain any transmembrane helices,
which complements the theory that the protein is not membrane bound, but rather cytoplasmic.
The KEGG, MetaCyc and E.C. databases all corroborate the identity of the query sequence as
succinyl-CoA synthetase alpha subunit in Thermoplasma acidophilum.
For this gene, no paralogs were found and the gene was not found to be present in any organism
outside of the Euryarachaeota Phylum. Therefore, it appears that this gene has not undergone any
horizontal gene transfer outside of the archael domain. The most distinct Euryarchaeota
containing the gene is the Aciduliprofundum organisms. Analysis of gene neighbourhood COG,
indicated that the genes, Succinyl-CoA synthetase alpha and beta subunits are conserved
between Aciduliprofundum, Thermoplasma, and Picrophilus organisms.
From the phylogentic tree, genes from related organisms such as Thermoplasma, Picrophilus,
Ferroplasma are clustered with one another. The Query from Ferroplasma clusters with the best
hits from Picrophilus and Thermoplasma. The next closest genes are those from
Aciduliprofundum and Methanohalophilus which are the next closest related genomes to the
Ferroplasma genome, so there is no evidence to suggest that this gene has recently undergone
HGT.
Conclusion:
Our findings supported a new function for gene OID 638394059 coding the alpha subunit of a
succinyl-CoA synthetase in F. acidarmanus Fer1.
Field: literature_links
Author: genbank
Date: Wed Nov 05 17:12:01 UTC 2014
1. Solow, B., Bischoff, K. M., Zylka, M. J., & Kennelly, P. J. (1998). Archaeal
phosphoproteins. Identification of a hexosephosphate mutase and the α‐subunit of
succinyl‐CoA synthetase in the extreme acidothermophile Sulfolobus solfataricus.
Protein science, 7(1), 105-111.
Field: synonyms
Author: genbank
IMG OID 638394059, succinyl-CoA synthetase
Field: gene_coordinates
Author: genbank
The gene OID 638394059 (519bp) is located at locus 1712840..1713694 (+) and codes for 284
amino acids with an isoelectric point of 7.03.
The Gene Caller identified one Shine-Dalgarno (SD) sequence upstream of the original start
codon. No alternative start codon with SD sequence was manually detected.