3ETC

2.1 A structure of acyl-adenylate synthetase from Methanosarcina acetivorans containing a link between Lys256 and Cys298

Summary for 3ETC

• Entry DOI: 10.2210/pdb3etc/pdb
• Descriptor: AMP-binding protein, FORMYL GROUP, TRIETHYLENE GLYCOL, ... (9 entities in total)
• Functional Keywords: adenylate-forming acyl-coa synthetase ligase, ligase
• Biological source: Methanosarcina acetivorans
• Total number of polymer chains: 2
• Total formula weight: 134981.05

Authors

Shah, M.B.,Gulick, A.M.,Smith, K.S.,Ingram-Smith, C. (deposition date: 2008-10-07, release date: 2009-07-07, Last modification date: 2023-12-27)

Primary citation

Shah, M.B.,Ingram-Smith, C.,Cooper, L.L.,Qu, J.,Meng, Y.,Smith, K.S.,Gulick, A.M.
The 2.1 A crystal structure of an acyl-CoA synthetase from Methanosarcina acetivorans reveals an alternate acyl-binding pocket for small branched acyl substrates.
Proteins, 77:685-698, 2009

PubMed Abstract: The acyl-AMP forming family of adenylating enzymes catalyze two-step reactions to activate a carboxylate with the chemical energy derived from ATP hydrolysis. X-ray crystal structures have been determined for multiple members of this family and, together with biochemical studies, provide insights into the active site and catalytic mechanisms used by these enzymes. These studies have shown that the enzymes use a domain rotation of 140 degrees to reconfigure a single active site to catalyze the two partial reactions. We present here the crystal structure of a new medium chain acyl-CoA synthetase from Methanosarcina acetivorans. The binding pocket for the three substrates is analyzed, with many conserved residues present in the AMP binding pocket. The CoA binding pocket is compared to the pockets of both acetyl-CoA synthetase and 4-chlorobenzoate:CoA ligase. Most interestingly, the acyl-binding pocket of the new structure is compared with other acyl- and aryl-CoA synthetases. A comparison of the acyl-binding pocket of the acyl-CoA synthetase from M. acetivorans with other structures identifies a shallow pocket that is used to bind the medium chain carboxylates. These insights emphasize the high sequence and structural diversity among this family in the area of the acyl-binding pocket.

PubMed: 19544569
DOI: 10.1002/prot.22482

Experimental method

X-RAY DIFFRACTION (2.1 Å)