ISDA: 6ZAF

Deposition Date 2020-06-05

Release Date 2021-06-09

Last Version Date 2024-01-24

Entry Detail

PDB ID:

6ZAF

Keywords:

OXIDOREDUCTASE

Title:

Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and ACV after exposure to dioxygen for 400ms.

Biological Source:

Source Organism(s):

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Taxon ID: 227321)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.40 Å

R-Value Free:

0.20

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Isopenicillin N synthase
Gene (Uniprot):ipnA
Chain IDs:A
Chain Length:331
Number of Molecules:1
Biological Source:Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)

UniProt ID:P05326 Pfam ID:PF14226, PF03171 EC:1.21.3.1

Ligand Molecules

ACV

FE2

SO4

Primary Citation

X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis.

Rabe, P, Kamps, J.J.A.G, Sutherlin, K.D, Linyard, J.D.S, Aller, P, Pham, C.C, Makita, H, Clifton, I, McDonough, M.A, Leissing, T.M, Shutin, D, Lang, P.A, Butryn, A, Brem, J, Gul, S, Fuller, F.D, Kim, I.S, Cheah, M.H, Fransson, T, Bhowmick, A, Young, I.D, O'Riordan, L, Brewster, A.S, Pettinati, I, Doyle, M, Joti, Y, Owada, S, Tono, K, Batyuk, A, Hunter, M.S, Alonso-Mori, R, Bergmann, U, Owen, R.L, Sauter, N.K, Claridge, T.D.W, Robinson, C.V, Yachandra, V.K, Yano, J, Kern, J.F, Orville, A.M, Schofield, C.J.Show

Sci Adv 7 ? ? (2021)

PMID: 34417180 DOI: 10.1126/sciadv.abh0250

Abstact

Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.

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Primary Citation of related structures

Abstact

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