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  Topic: Uncommon Dissent: Intellectuals Who Find Darwinism, Comments, links, etc.< Next Oldest | Next Newest >  

Posts: 319
Joined: May 2002

(Permalink) Posted: July 24 2003,22:51   


The bridge metaphor is pretty misleading, as M-H documented that functional organisms can exist without the full TCA cycle, that "shortcuts" across the cycle exist, etc.

But, since you asked, it appears that succinyl-CoA synthetase is part of a family of related enzymes:

Pfam CoA-ligase family entry

This article says that succinyl-CoA synthetase is homologous to acetyl-CoA synthetases and acyl-CoA synthetases:


J Biol Chem. 2000 Feb 25;275(8):5794-803.  
Acetyl-CoA synthetase from the amitochondriate eukaryote Giardia lamblia belongs to the newly recognized superfamily of acyl-CoA synthetases (Nucleoside diphosphate-forming).

Sanchez LB, Galperin MY, Muller M.

The gene coding for the acetyl-CoA synthetase (ADP-forming) from the amitochondriate eukaryote Giardia lamblia has been expressed in Escherichia coli. The recombinant enzyme exhibited the same substrate specificity as the native enzyme, utilizing acetyl-CoA and adenine nucleotides as preferred substrates and less efficiently, propionyl- and succinyl-CoA. N- and C-terminal parts of the G. lamblia acetyl-CoA synthetase sequence were found to be homologous to the alpha- and beta-subunits, respectively, of succinyl-CoA synthetase. Sequence analysis of homologous enzymes from various bacteria, archaea, and the eukaryote, Plasmodium falciparum, identified conserved features in their organization, which allowed us to delineate a new superfamily of acyl-CoA synthetases (nucleoside diphosphate-forming) and its signature motifs. The representatives of this new superfamily of thiokinases vary in their domain arrangement, some consisting of separate alpha- and beta-subunits and others comprising fusion proteins in alpha-beta or beta-alpha orientation. The presence of homologs of acetyl-CoA synthetase (ADP-forming) in such human pathogens as G. lamblia, Yersinia pestis, Bordetella pertussis, Pseudomonas aeruginosa, Vibrio cholerae, Salmonella typhi, Porphyromonas gingivalis, and the malaria agent P. falciparum suggests that they might be used as potential drug targets.
...and this article is about the origin of acetyl-CoA synthase:


Orig Life Evol Biosph. 2001 Aug-Oct;31(4-5):403-34.

The evolution of acetyl-CoA synthase.

Lindahl PA, Chang B.

Acetyl-coenzyme A synthases (ACS) are Ni-Fe-S containing enzymes found in archaea and bacteria. They are divisible into 4 classes. Class I ACS's catalyze the synthesis of acetyl-CoA from CO2 + 2e-, CoA, and a methyl group, and contain 5 types of subunits (alpha, beta, gamma, delta, and epsilon). Class II enzymes catalyze essentially the reverse reaction and have similar subunit composition. Class III ACS's catalyze the same reaction as Class I enzymes, but use pyruvate as a source of CO2 and 2e-, and are composed of 2 autonomous proteins, an alpha 2 beta 2 tetramer and a gamma delta heterodimer. Class IV enzymes catabolize CO to CO2 and are alpha-subunit monomers. Phylogenetic analyses were performed on all five subunits. ACS alpha sequences divided into 2 major groups, including Class I/II sequences and Class III/IV-like sequences. Conserved residues that may function as ligands to the B- and C-clusters were identified. Other residues exclusively conserved in Class I/II sequences may be ligands to additional metal centers in Class I and II enzymes. ACS beta sequences also separated into two groups, but they were less divergent than the alpha's, and the separation was not as distinct. Class III-like beta sequences contained approximately 300 residues at their N-termini absent in Class I/II sequences. Conserved residues identified in beta sequences may function as ligands to active site residues used for acetyl-CoA synthesis. ACS gamma-sequences separated into 3 groups (Classes I, II, and III), while delta-sequences separated into 2 groups (Class I/II and III). These groups are less divergent than those of alpha sequences. ACS epsilon-sequence topology showed greater divergence and less consistency vis-a-vis the other subunits, possibly reflecting reduced evolutionary constraints due to the absence of metal centers. The alpha subunit phylogeny may best reflect the functional diversity of ACS enzymes. Scenarios of how ACS and ACS-containing organisms may have evolved are discussed.
Or, we could just note that the CoA ligase family includes ATP-citrate lyase, which is a component of the rest of the TCA cycle.

(all of this is assuming I'm not making a terminological mistake somewhere, the naming of components is a bit confusing as enzymes get called different things depending on which way the reaction is being run, etc.)

Conclusion: succinyl-CoA synthetase didn't come from nowhere, homologous enzymes were present before the TCA cycle was completed.

PS: Dembski, I believe, raised this same argument in one of his debates with Ken Miller/Wes Elsberry.  Why didn't he look for the above literature first?

  11 replies since July 22 2003,20:51 < Next Oldest | Next Newest >  


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