7TGL | pdb_00007tgl

Crystal structure of AMP+PPi bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway

PDB DOI: https://doi.org/10.2210/pdb7TGL/pdb

Classification: LIGASE
Organism(s): Streptomyces griseoflavus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-07 Released: 2022-07-06
Deposition Author(s): Patel, K.D., Gulick, A.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.189 (Depositor), 0.194 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD.

Yang, J., Banas, V.S., Patel, K.D., Rivera, G.S.M., Mydy, L.S., Gulick, A.M., Wencewicz, T.A.

(2022) J Biological Chem 298: 102166-102166

PubMed: 35750210 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2022.102166
Primary Citation Related Structures:
7TGJ, 7TGK, 7TGL, 7TGM, 7TGN

PubMed Abstract:
Siderophores are conditionally essential metabolites used by microbes for environmental iron sequestration. Most Streptomyces strains produce hydroxamate-based desferrioxamine (DFO) siderophores composed of repeating units of N ¹-hydroxy-cadaverine (or N ¹-hydroxy-putrescine) and succinate. The DFO biosynthetic operon, desABCD, is highly conserved in Streptomyces; however, expression of desABCD alone does not account for the vast structural diversity within this natural product class. Here, we report the in vitro reconstitution and biochemical characterization of four DesD orthologs from Streptomyces strains that produce unique DFO siderophores. Under in vitro conditions, all four DesD orthologs displayed similar saturation steady-state kinetics (V _max = 0.9-2.5 μM⋅min ^-1) and produced the macrocyclic trimer DFOE as the favored product, suggesting a conserved role for DesD in the biosynthesis of DFO siderophores. We further synthesized a structural mimic of N ¹-hydroxy-N ¹-succinyl-cadaverine (HSC)-acyl-adenylate, the HSC-acyl sulfamoyl adenosine analog (HSC-AMS), and obtained crystal structures of DesD in the ATP-bound, AMP/PP _i-bound, and HSC-AMS/P _i-bound forms. We found HSC-AMS inhibited DesD orthologs (IC ₅₀ values = 48-53 μM) leading to accumulation of linear trimeric DFOG and di-HSC at the expense of macrocyclic DFOE. Addition of exogenous PP _i enhanced DesD inhibition by HSC-AMS, presumably via stabilization of the DesD-HSC-AMS complex, similar to the proposed mode of adenylate stabilization where PP _i remains buried in the active site. In conclusion, our data suggest that acyl-AMS derivatives may have utility as chemical probes and bisubstrate inhibitors to reveal valuable mechanistic and structural insight for this unique family of adenylating enzymes.

Organizational Affiliation

Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA.

Macromolecule Content

Total Structure Weight: 348.73 kDa
Atom Count: 23,630
Modeled Residue Count: 2,955
Deposited Residue Count: 3,060
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Desferrioxamine synthetase DesD	A, B, C, D, E	612	Streptomyces griseoflavus	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain RA [auth E] SDF format, chain S [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B]	BA [auth C], HA [auth D], I [auth A], RA [auth E], S [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain BA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain RA [auth E] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain RA [auth E] Focus chain S [auth B]
PPV (Subject of Investigation/LOI) Query on PPV Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain QA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth E] mmCIF format, chain AA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth E]	AA [auth C], GA [auth D], H [auth A], QA [auth E], R [auth B]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain QA [auth E] Focus chain R [auth B] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain QA [auth E] Focus chain R [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain SA [auth E] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain SA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	IA [auth D] J [auth A] JA [auth D] KA [auth D] SA [auth E] IA [auth D], J [auth A], JA [auth D], KA [auth D], SA [auth E], T [auth B], U [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain SA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain SA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain NA [auth E] SDF format, chain P [auth B] SDF format, chain PA [auth E] SDF format, chain Q [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain OA [auth E] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain OA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain OA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain FA [auth D]	EA [auth D] F [auth A] FA [auth D] G [auth A] M [auth B] EA [auth D], F [auth A], FA [auth D], G [auth A], M [auth B], N [auth B], NA [auth E], O [auth B], OA [auth E], P [auth B], PA [auth E], Q [auth B], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain NA [auth E] Focus chain O [auth B] Focus chain OA [auth E] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain NA [auth E] Focus chain O [auth B] Focus chain OA [auth E] Focus chain P [auth B] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain K [auth A] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain L [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain L [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain L [auth A]	CA [auth C] DA [auth C] K [auth A] L [auth A] LA [auth D] CA [auth C], DA [auth C], K [auth A], L [auth A], LA [auth D], MA [auth D], TA [auth E], UA [auth E], W [auth B], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain W [auth B] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.235 (Depositor), 0.235 (DCC)
R-Value Work: 0.189 (Depositor), 0.194 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.501	α = 90
b = 236.745	β = 90
c = 330.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Patel, K.D.

Gulick, A.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM136235
National Science Foundation (NSF, United States)	United States	1654611