ADP-Binding Site of <i>Escherichia coli</i> Succinyl-CoA Synthetase Revealed by X-ray Crystallography<sup>,</sup>

Joyce, Michael; Fraser, M.E.; James, Michael N.G.; Bridger, William A.; Wolodko, William T.

doi:10.1021/bi991696f

Cited by 45 publications

(60 citation statements)

References 32 publications

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“…The movement of the phosphohistidine loop with phosphorylated catalytic histidine has been suggested to shuttle the phosphate between the active sites of both subunits. 14,15 The missing fragment in the case of skipping of exon 6 and part of exon 7, encompassing residues 221-267, contains Glu256, a critical residue for ADP phosphorylation. 21 Location of Asp333, a part of 'power' helix b and the interface between subunits, within the modeled human mitochondrial SCS-A (b).…”

Section: Discussionmentioning

confidence: 99%

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Mitochondrial encephalomyopathy and retinoblastoma explained by compound heterozygosity of SUCLA2 point mutation and 13q14 deletion

et al. 2014

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Mutations in SUCLA2, encoding the -subunit of succinyl-CoA synthetase of Krebs cycle, are one cause of mitochondrial DNA depletion syndrome. Patients have been reported to have severe progressive childhood-onset encephalomyopathy, and methylmalonic aciduria, often leading to death in childhood. We studied two families, with children manifesting with slowly progressive mitochondrial encephalomyopathy, hearing impairment and transient methylmalonic aciduria, without mtDNA depletion. The other family also showed dominant inheritance of bilateral retinoblastoma, which coexisted with mitochondrial encephalomyopathy in one patient. We found a variant in SUCLA2 leading to Asp333Gly change, homozygous in one patient and compound heterozygous in one. The latter patient also carried a deletion of 13q14 of the other allele, discovered with molecular karyotyping. The deletion spanned both SUCLA2 and RB1 gene regions, leading to manifestation of both mitochondrial disease and retinoblastoma. We made a homology model for human succinyl-CoA synthetase and used it for structure-function analysis of all reported pathogenic mutations in SUCLA2. On the basis of our model, all previously described mutations were predicted to result in decreased amounts of incorrectly assembled protein or disruption of ADP phosphorylation, explaining the severe early lethal manifestations. However, the Asp333Gly change was predicted to reduce the activity of the otherwise functional enzyme. On the basis of our findings, SUCLA2 mutations should be analyzed in patients with slowly progressive encephalomyopathy, even in the absence of methylmalonic aciduria or mitochondrial DNA depletion. In addition, an encephalomyopathy in a patient with retinoblastoma suggests mutations affecting SUCLA2.

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Section: Discussionmentioning

confidence: 99%

“…(Figure 3; PDB id 1CQI). 15 The protein model indicated the organization of the SCS-A, with ATP-and succinylCoA-binding sites located on the opposite sides of the heterodimer (Figure 3a). We mapped all the known SUCLA2 mutations into the protein model.…”

Section: Quantification Of Mtdnamentioning

confidence: 99%

Mitochondrial encephalomyopathy and retinoblastoma explained by compound heterozygosity of SUCLA2 point mutation and 13q14 deletion

et al. 2014

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“…In the case of CoA thioester formation by SCS Ec , the ␥-phosphate of ATP is first transferred to the catalytic His 246 residue in the ␣-subunit, and the phosphorylated imidazole ring reacts with acid and CoA to form the corresponding acyl-CoA molecule. The ATP-and CoA-binding sites are located within the ATP-grasp fold domain in the ␤-subunit (domains 3-4) and the CoA-binding domain in the ␣-subunit (domain 1), respectively (23,27,30,31). The catalytic His residue (corresponding to His 261 in the TK1880 ␣-subunit) and several important residues that function in binding with the ATP⅐Mg 2ϩ complex and CoA are well conserved among this superfamily (18).…”

Section: Discussionmentioning

confidence: 99%

A Novel ADP-forming Succinyl-CoA Synthetase in Thermococcus kodakaraensis Structurally Related to the Archaeal Nucleoside Diphosphate-forming Acetyl-CoA Synthetases

Shikata

Fukui

Atomi

et al. 2007

Journal of Biological Chemistry

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We have identified and characterized a structurally novel succinyl-CoA synthetase (SCS) from the hyperthermophilic Archaea Thermococcus kodakaraensis. The presence of an SCS completes the metabolic pathway from glutamate to succinate in Thermococcales, which had not been clarified because of the absence of classical SCS homologs on their genomes. The SCS from T. kodakaraensis (SCS Tk ) is a heteromeric enzyme (␣ 2 ␤ 2 ) encoded by TK1880 (␣-subunit) and TK0943 (␤-subunit). Although both SCS Tk and classical SCSs harbor the five domains present in enzymes of the acyl-CoA synthetase (nucleoside diphosphate-forming) superfamily, the domain order and distribution among subunits in SCS Tk (␣-subunit, domains 1-2-5; ␤-subunit, domains 3-4) are distinct from those of classical SCSs (␣-subunit, domains 1-2; ␤-subunit, domains 3-4-5) and instead resemble the acetyl-CoA synthetases from Pyrococcus furiosus (ACSs I Pf and II Pf ). Comparison of the four Thermococcales genomes revealed that each strain harbors five ␣-and two ␤-subunit homologs. Sequence similarity suggests that the ␤-subunit of SCS Tk is also a component of the presumed ACS II from T. kodakaraensis (ACS II Tk ). We coexpressed the ␣/␤-genes of SCS Tk (TK1880/TK0943) and of ACS II Tk (TK0139/ TK0943). ACS II Tk recognizes a broad range of hydrophobic/ aromatic acid compounds, as is the case with ACS II Pf , whereas SCS Tk displays a distinct and relatively strict substrate specificity for several acids, including succinate. This indicates that the ␣-subunits are responsible for the distinct substrate specificities of SCS Tk and ACS II Tk .Thermococcus and Pyrococcus species are hyperthermophilic Archaea that preferentially utilize peptides/amino acids for cell growth (1). It is presumed that amino acids are first deaminated to 2-oxo acids by aminotransferases, with 2-oxoglutarate as a key amino acceptor (2). The generated glutamate is converted back to 2-oxoglutarate by oxidative deamination catalyzed by glutamate dehydrogenase (3). The 2-oxo acids are then converted to CoA thioester compounds by oxidative decarboxylation. Ferredoxin-dependent oxidoreductases catalyze these reactions, and a number of enzymes with distinct substrate specificities have been identified in Pyrococcus furiosus (4 -7). Closely related genes are also found on the genomes of Thermococcus kodakaraensis (8), Pyrococcus abyssi (9), and Pyrococcus horikoshii (10). The final step is the hydrolysis of the thioester bond, releasing a carboxylic acid and CoA accompanied by substrate level phosphorylation, an important energy conservation reaction in these hyperthermophiles. The ADP-forming acetyl-CoA synthetases I and II from P. furiosus (ACSs I Pf 2 and II Pf ) have been identified to be involved in this step (11-14) and exhibit activity not only for acetyl-CoA but also for branched-chain acyl-CoAs (ACSs I Pf and II Pf ) and aryl-CoAs (ACS II Pf ) (13). The substrate specificities of the two enzymes are consistent with the preferential consumption of Leu, Ile, and Phe by P. furiosus during...

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“…This phenomenon, termed "domain shuffling," is one of the key features of this superfamily (8). Superposition of several structures of SCS from Escherichia coli (ecSCS) (12)(13)(14), Thermus aquaticus (15), the mammalian GTP-specific SCS from pig (16), and a truncated form of human ACLY (17,18) revealed that subdomains 1-5 share a common arrangement in these enzymes. From detailed studies of the reaction mechanism of ecSCS, a crucial enzyme tightly connected to the TCA cycle, a three-step mechanism was proposed, which involves the phosphorylation of a highly conserved His residue at the first active site (site I) as an intermediate step (12,13).…”

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confidence: 99%

“…Subsequently, the phosphoryl moiety is transferred onto an NDP that is bound at the second active site (site II). The distance of around 36 Å between site I and site II is assumed to be bridged by a so-called "swinging loop" (12,14,19). A mechanism comparable to the mechanism of the SCSs was presumed for the ACDs (20).…”

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confidence: 99%

Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer

Weisse

Faust

Schmidt

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The NDP-forming acyl-CoA synthetases (ACDs) catalyze the conversion of various CoA thioesters to the corresponding acids, conserving their chemical energy in form of ATP. The ACDs are the major energy-conserving enzymes in sugar and peptide fermentation of hyperthermophilic archaea. They are considered to be primordial enzymes of ATP synthesis in the early evolution of life. We present the first crystal structures, to our knowledge, of an ACD from the hyperthermophilic archaeon Candidatus Korachaeum cryptofilum. These structures reveal a unique arrangement of the ACD subunits alpha and beta within an α 2 β 2 -heterotetrameric complex. This arrangement significantly differs from other members of the superfamily. To transmit an activated phosphoryl moiety from the Ac-CoA binding site (within the alpha subunit) to the NDP-binding site (within the beta subunit), a distance of 51 Å has to be bridged. This transmission requires a larger rearrangement within the protein complex involving a 21-aa-long phosphohistidinecontaining segment of the alpha subunit. Spatial restraints of the interaction of this segment with the beta subunit explain the necessity for a second highly conserved His residue within the beta subunit. The data support the proposed four-step reaction mechanism of ACDs, coupling acyl-CoA thioesters with ATP synthesis. Furthermore, the determined crystal structure of the complex with bound Ac-CoA allows first insight, to our knowledge, into the determinants for acyl-CoA substrate specificity. The composition and size of loops protruding into the binding pocket of acyl-CoA are determined by the individual arrangement of the characteristic subdomains.X-ray structure | metabolic energy conversion | protein dynamics | acyl-coenzyme A thioester | superfamily N DP-forming acyl-CoA synthetases (ACDs) catalyze the conversion of acyl-CoA thioesters to the corresponding acids and couple this reaction with the synthesis of ATP via the mechanism of substrate-level phosphorylation. ACDs have been studied in detail in hyperthermophilic archaea, where they function as the major energy-conserving enzymes in the course of anaerobic sugar and peptide fermentation (1-4). It is believed that ACDs represent a primordial mechanism of ATP synthesis in the early evolution of life. ACDs were found in all acetate (acid)-forming archaea (5, 6) and in the eukaryotic parasitic protists Entamoeba histolytica (7) and Giardia lamblia (8), but they have not been found in acetate-forming bacteria. In bacteria, with the exception of Chloroflexus (9), the conversion of inorganic phosphate and the thioester acetyl (Ac)-CoA to acetate and ATP is catalyzed by two enzymes, phosphate Ac-transferase and acetate kinase (10).

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ADP-Binding Site of Escherichia coli Succinyl-CoA Synthetase Revealed by X-ray Crystallography^,

Cited by 45 publications

References 32 publications

Mitochondrial encephalomyopathy and retinoblastoma explained by compound heterozygosity of SUCLA2 point mutation and 13q14 deletion

Mitochondrial encephalomyopathy and retinoblastoma explained by compound heterozygosity of SUCLA2 point mutation and 13q14 deletion

A Novel ADP-forming Succinyl-CoA Synthetase in Thermococcus kodakaraensis Structurally Related to the Archaeal Nucleoside Diphosphate-forming Acetyl-CoA Synthetases

Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer

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ADP-Binding Site of Escherichia coli Succinyl-CoA Synthetase Revealed by X-ray Crystallography,

Cited by 45 publications

References 32 publications

Mitochondrial encephalomyopathy and retinoblastoma explained by compound heterozygosity of SUCLA2 point mutation and 13q14 deletion

Mitochondrial encephalomyopathy and retinoblastoma explained by compound heterozygosity of SUCLA2 point mutation and 13q14 deletion

A Novel ADP-forming Succinyl-CoA Synthetase in Thermococcus kodakaraensis Structurally Related to the Archaeal Nucleoside Diphosphate-forming Acetyl-CoA Synthetases

Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer

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ADP-Binding Site of Escherichia coli Succinyl-CoA Synthetase Revealed by X-ray Crystallography^,