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1.21.3.1: isopenicillin-N synthase

This is an abbreviated version!
For detailed information about isopenicillin-N synthase, go to the full flat file.

Word Map on EC 1.21.3.1

Reaction

N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine
+
O2
=
isopenicillin N
 + 2 H2O

Synonyms

IPN cyclase, IPN synthase, IPNS, isopenicillin N synthase, isopenicillin N synthase (cyclase), isopenicillin N synthetase, isopenicillin N-synthase, isopenicillin-N synthase, isopenicillin-N-synthase, More, PcbC, synthetase, isopenicillin N (9Cl)

ECTree

     1 Oxidoreductases
         1.21 Catalysing the reaction X-H + Y-H = X-Y
             1.21.3 With oxygen as acceptor
                1.21.3.1 isopenicillin-N synthase

Crystallization

Crystallization on EC 1.21.3.1 - isopenicillin-N synthase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of the enzyme reveals that the active site of IPNS is buried in a characteristic jelly-roll motif that has been found in other oxygenases
-
crystal structure of the enzyme in complex with substrate analoge delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-methionine and Fe(II) at 1.40 A resolution reveals that the compound binds in the active site such that the sulfur atom of the methionine thioether binds to iron in the oxygen binding site at a distance of 2.57 A. The sulfur of the cysteinyl thiolate sits 2.36 A from the metal
enzyme complexed with manganese instead of iron in the active site, more stable
in complex with substrat analogue delta-(L-alpha-aminoadipoyl)-L-cysteinyl-O-methyl-D-threonine and Fe(II). Structure reveals an additional water molecule bound to the active site metal, held by hydrogen-bonding to the ether oxygen atom of the substrate analogue
in complex with substrate analogue delta-(L-alpha-aminoadipoyl)-(3R)-methyl-L-cysteine D-alpha hydroxyvaleryl ester, crystallization with anaerobic conditions and exposure of crystals to oxygen giving a hydroxymethyl/ene product. Discussion of steric and electronic effects around the valinyl isopropyl side chain of the enzyme’s active side
in complex with substrate homologues delta-(L-alpha-aminoadipoyl)-L-homocysteinyl-D-valine and delta-(L-alpha-aminoadipoyl)-L-homocysteinyl-delta-S-methylcysteine. The complex with Fe(II) and delta-(L-alpha-aminoadipoyl)-L-homocysteinyl-D-valine shows diffuse electron density for several regions of the substrate, revealing considerable conformational freedom within the active site. The substrate is more clearly resolved in the complex delta-(L-alpha-aminoadipoyl)-L-homocysteinyl-delta-S-methylcysteine by virtue of thioether coordination to iron. delta-(L-alpha-aminoadipoyl)-L-homocysteinyl-delta-S-methylcysteine occupies two distinct conformations, both distorted relative to the natural substrate (L-alha-aminoadipoyl)-L-cysteinyl-D-valine, in order to accommodate the extra methylene group in the second residue
in complex with tripeptyl analogues delta-(L-alpha-aminoadipoyl)-L-cysteinyl-beta-methyl-D-cyclopropylglycine and delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-cyclopropylglycine, crystallization in presence of Fe-(II) under anaerobic conditions
in complex with truncated substrate analogues delta-(L-alpha-aminoadipoyl)-L-cysteinyl-glycine and delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-alanine in presence of Fe(II) and presence and absence of nitric oxide. C-terminal carboxylate of substrate is oriented toward the active site iron atom
structure analysis
the crystal structures of isopenicillin N synthase in complex with gamma-(L-alpha-aminoadipoyl)-(3S-methyl)-L-cysteine D-alpha-hydroxyisovaleryl ester and FeII exposed to O2 and unexposed to O2 are solved to resolutions of 2.2 and 1.65 A, respectively
the crystal structures of isopenicillin N synthase in complex with L-alpha-aminoadipoyl-L-cysteine (1-(S)-carboxy-2-thiomethyl)ethyl ester and FeII exposed to O2 and unexposed to O2 are determined to 1.4 and 1.8 A resolutions, respectively
-
crystal structure, molecular modeling of the active site structure and the Fe2+-binding motif
-