6GEH | pdb_00006geh

Structure and reactivity of a siderophore-interacting protein from the marine bacterium Shewanella reveals unanticipated functional versatility.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 
    0.173 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure and reactivity of a siderophore-interacting protein from the marine bacteriumShewanellareveals unanticipated functional versatility.

Trindade, I.B.Silva, J.M.Fonseca, B.M.Catarino, T.Fujita, M.Matias, P.M.Moe, E.Louro, R.O.

(2019) J Biological Chem 294: 157-167

  • DOI: https://doi.org/10.1074/jbc.RA118.005041
  • Primary Citation Related Structures: 
    6GEH

  • PubMed Abstract: 

    Siderophores make iron accessible under iron-limited conditions and play a crucial role in the survival of microorganisms. Because of their remarkable metal-scavenging properties and ease in crossing cellular envelopes, siderophores hold great potential in biotechnological applications, raising the need for a deeper knowledge of the molecular mechanisms underpinning the siderophore pathway. Here, we report the structural and functional characterization of a siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIBM400 (SfSIP). SfSIP is a flavin-containing ferric-siderophore reductase with FAD- and NAD(P)H-binding domains that have high homology with other characterized SIPs. However, we found here that it mechanistically departs from what has been described for this family of proteins. Unlike other FAD-containing SIPs, SfSIP did not discriminate between NADH and NADPH. Furthermore, SfSIP required the presence of the Fe 2+ -scavenger, ferrozine, to use NAD(P)H to drive the reduction of Shewanella -produced hydroxamate ferric-siderophores. Additionally, this is the first SIP reported that also uses a ferredoxin as electron donor, and in contrast to NAD(P)H, its utilization did not require the mediation of ferrozine, and electron transfer occurred at fast rates. Finally, FAD oxidation was thermodynamically coupled to deprotonation at physiological pH values, enhancing the solubility of ferrous iron. On the basis of these results and the location of the SfSIP gene downstream of a sequence for putative binding of aerobic respiration control protein A (ArcA), we propose that SfSIP contributes an additional layer of regulation that maintains cellular iron homeostasis according to environmental cues of oxygen availability and cellular iron demand.


  • Organizational Affiliation
    • Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157 Oeiras, Portugal.

Macromolecule Content 

  • Total Structure Weight: 30.36 kDa 
  • Atom Count: 2,865 
  • Modeled Residue Count: 256 
  • Deposited Residue Count: 256 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FAD-binding 9, siderophore-interacting domain protein256Shewanella frigidimarina NCIMB 400Mutation(s): 0 
Gene Names: Sfri_2392
EC: 1.16
UniProt
Find proteins for Q080S8 (Shewanella frigidimarina (strain NCIMB 400))
Explore Q080S8 
Go to UniProtKB:  Q080S8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ080S8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
JA [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
IA [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free:  0.173 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.098α = 90
b = 77.753β = 109.64
c = 44.917γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentPortugalxx

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description