The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of siderophore-interacting protein (ZP_00813641.1) from Shewanella putrefaciens CN-32 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 2gpj Target Id 361165
    Molecular Characteristics
    Source Shewanella putrefaciens cn-32
    Alias Ids TPS1463,YP_001181611.1, PF04954, PF08021, 90706 Molecular Weight 28004.52 Da.
    Residues 251 Isoelectric Point 5.37
    Sequence mmnkpaprelevirstyitphmlritlggaglagfpadqesayikllfpqagerplmrtytirqqrdde idvdfvlhdtdgpasswaktaqvgeliqiggpglkklinfeadwfllagdmtalpaisvnlaklpnnav gyavievlseadiqplvhpehvelhwvinpeadpegrplveriaqlpwlagepavwiacefnsmralrr hfkqahalpkshfytssywkigcnegehklvkqedeqlengasv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.20 Rfree 0.232
    Matthews' coefficent 2.84 Rfactor 0.176
    Waters 96 Solvent Content 56.36

    Ligand Information


    Google Scholar output for 2gpj
    1. Siderophore-based iron acquisition and pathogen control
    M Miethke, MA Marahiel - Microbiology and Molecular Biology , 2007 - Am Soc Microbiol
    2. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    3. The Mycobacterium tuberculosis high-affinity iron importer, IrtA, contains an FAD-binding domain
    MB Ryndak, S Wang, I Smith - Journal of , 2010 - Am Soc Microbiol
    4. Preliminary X-ray diffraction analysis of YqjH from Escherichia coli: a putative cytoplasmic ferri-siderophore reductase
    VA Bamford, M Armour, SA Mitchell - Section F: Structural , 2008 - scripts.iucr.org
    5. The Siderophore-Interacting Protein YqjH Acts as a Ferric Reductase in Different Iron Assimilation Pathways of Escherichia coli
    M Miethke, J Hou, MA Marahiel - Biochemistry, 2011 - ACS Publications

    Protein Summary

    Gene Sputcn32_0076 from Shewanella putrefaciens cn-32 encodes the YP_001181611 protein with two domains belonging, the N-terminal to the siderophore interacting FAD binding group (PF08021), and the C-terminal to the siderophore interacting group (PF04954).

    Siderophores are are molecules with high affinity for iron ions that are secreted by bacteria and other mocroorganisms and reimported as metal complexes in order to provide the cell with a supply of iron from the environment. Siderophore-interacting proteins are subsequently involved in the release and re-utilization of iron inside the cell. This is so far the only example of a siderophore interacting protein present in the pdb. The crystallization and preliminary analysis of another YqjH from Escherichia coli has also been reported [Ref].

    Pre-SCOP classifies 2gpj in the all beta class, riboflavin synthase domain-like superfamily. DALI top hits with 2gpj are ferredoxin NADP reductases 3jqr, 2r6h and 1a8p (Z=18).
    This siderophore-interacting structure (2gpj) from Shewanella putrefaciens CN-32 consists of two globular domains- an N-terminal FAD binding domain and a C-terminal NADPH binding domain. The FAD binding domain is a double sandwich beta-domain structurally similar to the FAD binding domains of the ferredoxin reductase family. The NADPH binding domain structure is similar to dehydrogenases with a Rossmann fold topology. The protein structure includes a molecule of FAD which binds in a cleft formed by the two domains. The flavin moiety of the FAD molecule extends into a hydrophobic groove and is sequestered by aromatic residues including Tyr43, Tyr60, and Tyr225. The adenine portion of the molecule pi-stacks with Trp226, causing a bent conformation of the FAD molecule. This structure most closely resembles E. coli flavodoxin reductase (1FDR, Z=18). Based on structural and sequence homology, siderophore-interacting protein YP_001181611 from Shewanella putrefaciens CN-32 belongs to the superfamily of ferredoxin reductases and is most likely involved in electron transport between flavodoxin or ferredoxin and NADPH.

    Ligand Summary





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