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Structure paper

TitleStructural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 5097, Year 2022
Publish dateAug 30, 2022
AuthorsTakuya Miyakawa / Jian Yang / Masato Kawasaki / Naruhiko Adachi / Ayumu Fujii / Yumiko Miyauchi / Tomonari Muramatsu / Toshio Moriya / Toshiya Senda / Masaru Tanokura /
PubMed AbstractCyanophycin is a natural biopolymer consisting of equimolar amounts of aspartate and arginine as the backbone and branched sidechain, respectively. It is produced by a single enzyme, cyanophycin ...Cyanophycin is a natural biopolymer consisting of equimolar amounts of aspartate and arginine as the backbone and branched sidechain, respectively. It is produced by a single enzyme, cyanophycin synthetase (CphA1), and accumulates as a nitrogen reservoir during N fixation by most cyanobacteria. A recent structural study showed that three constituent domains of CphA1 function as two distinct catalytic sites and an oligomerization interface in cyanophycin synthesis. However, it remains unclear how the ATP-dependent addition of aspartate to cyanophycin is initiated at the catalytic site of the glutathione synthetase-like domain. Here, we report the cryogenic electron microscopy structures of CphA1, including a complex with aspartate, cyanophycin primer peptide, and ATP analog. These structures reveal the aspartate binding mode and phosphate-binding loop movement to the active site required for the reaction. Furthermore, structural and mutational data show a potential role of protein dynamics in the catalytic efficiency of the arginine condensation reaction.
External linksNat Commun / PubMed:36042318 / PubMed Central
MethodsEM (single particle)
Resolution2.52 - 2.96 Å
Structure data

32381

7wac

EMDB-32381, PDB-7wac:
Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1)
Method: EM (single particle) / Resolution: 2.91 Å

32382

7wad

EMDB-32382, PDB-7wad:
Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS
Method: EM (single particle) / Resolution: 2.96 Å

32383

7wae

EMDB-32383, PDB-7wae:
Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS, 4x(beta-Asp-Arg), and aspartate
Method: EM (single particle) / Resolution: 2.64 Å

32384

7waf

EMDB-32384, PDB-7waf:
Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS and 4x(beta-Asp-Arg)
Method: EM (single particle) / Resolution: 2.52 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-ASP:
ASPARTIC ACID

ChemComp-ARG:
ARGININE

Source
  • trichodesmium erythraeum ims101 (bacteria)
  • synthetic construct (others)
KeywordsLIGASE / Cyanophycin / Non-ribosomal peptide synthesis / ATP / Aspartate / Arginine

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