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The Open Protein Structure Annotation Network
PDB Keyword
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3hn0

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of Nitrate transport protein (YP_001302749.1) from Parabacteroides distasonis ATCC 8503 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 3hn0 Target Id 394807
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25382,YP_001302749.1 Molecular Weight 31254.44 Da.
    Residues 282 Isoelectric Point 7.58
    Sequence tedtvikvsvlrgpsviafadwlenppiidnkkvqvkvvdspdlaqallikqetdiavlpminaanlyn kgikiklagcpiwgtlylvektplkepalyvfgngttpdiltryylgrqrldyplnyafntageitqgi lagkvnravlgepflsialrkdsslritadlnhltdndtlgfaqtavvytptmekyriafedalrascq kavrypketihsleehgifaqgaltpksierckiyylsaieakdavmgflrlieqyepkavggrlpdag fipekq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.75 Rfree 0.210
    Matthews' coefficent 2.11 Rfactor 0.170
    Waters 601 Solvent Content 41.63

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hn0
    1. A structural classification of substrate-binding proteins
    RPA Berntsson, SHJ Smits, L Schmitt, DJ Slotboom - FEBS letters, 2010 - Elsevier
     
    2. A structural classification of substrate-binding proteins
    PAB Ronnie, SHJ Smits, L Schmitt, DJ Slotboom - FEBS , 2010 - gbb.eldoc.ub.rug.nl
     

    Protein Summary

    BDI_1369 gene from Parabacteroides distasonis (a gram-negative bacteria found that is commonly found in mammalian gastrointestinal flora) encodes the YP_001302749 protein that belongs to the DUF411 group (PF04214), some members of which are thought to confer cation resistance. The sequence overlaps with Pfam PF09084, members of which are periplasmic binding proteins. Its genomic neighbor, BDI_1370, is annotated as putative ABC transporter (score 0.9).

    The 3hn0 structure, solved by Se-MAD to a resolution of 1.75 Angstroms, adopts an alpha/beta fold consisting of two globule domains (Figure 1ab).  fastSCOP analysis assigned 3hn0 inside the alpha/beta class, the fold as belonging to the periplasmic binding protein-like IIsuperfamily, phosphate binding protein-like family. Some members of the structural superfamily belong to an ATP-binding cassette (ABC) transporter operon.  Based on analytical size exclusion chromatography (anSEC) results and also the putative role of the protein as an ABC transporter periplasmic binding protein, YP_001302749.1 most likely functions as a monomer.

     

    Figure 1.  Structure of a monomer of 3hn0 (left) rainbow colored from N-terminus (blue) to C-terminus (red) and (right) showing the two different domains (green and purple) that together form a C-shaped clamp.

    GS13941A-monomer.pngGS13941A-monomer-2.png

     

    Sequence (BLAST and FFAS) and structural (DALI and SSM) comparisons all point towards the notion that YP_001302749.1 may be a binding protein in an ABC transporter system. (Tables 1 and 2).  STRING analysis further supports this idea, as the most closely associated protein found for YP_001302749.1 was a putative ABC-transporter (also from Parabacteroides distasonis).  When this putative ABC transporter was analyzed with BLAST, some of the resulting stronger sequence homologs were ABC transporters for nitrate, aliphatic sulfonates, and iron (III).

     

    Table 1.  Dali structural similarity search results using 3hn0 as query:

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2i4b 21.9 3.2 264 401 11 BICARBONATE TRANSPORTER
    2 3e4r 21.8 3.6 262 291 11 NITRATE TRANSPORT PROTEIN
    3 2g29 21.4 3.5 264 385 13 NITRATE TRANSPORT PROTEIN NRTA
    4 2czl 20.3 3.8 247 270 13 HYPOTHETICAL PROTEIN TTHA1568
    5 2qpq 15.4 3.4 224 296 10 PROTEIN BUG27
    6 2de2 15.2 3.4 246 347 7 DIBENZOTHIOPHENE DESULFURIZATION ENZYME B
    7 2dvz 14.3 3.3 219 300 7 PUTATIVE EXPORTED PROTEIN
    8 1xs5 13.5 3.0 199 240 10 MEMBRANE LIPOPROTEIN TPN32
    9 1p99 13.5 3.5 214 255 14 HYPOTHETICAL PROTEIN PG110
    10 3cvg 12.5 4.0 209 270 6 PUTATIVE METAL BINDING PROTEIN

     

    Table 2.  SSM structurare similarity search results using 3hn0 as query:

    N PDB Q-score RMSD TITLE
    1 3e4r 0.3468 3.032 THE ALKANESULFONATE BINDING PROTEIN (SSUA) FROM THE PHYTOPATHOGENIC BACTERIA XANTHOMONAS AXONOPODIS PV. CITRI BOUND TO HEPES
    2 2dbp 0.3019 3.338 A CONSERVED HYPOTHETICAL PROTEIN TTHA1568 FROM THERMUS THERMOPHILUS HB8
    3 2czl 0.2951 3.326 CONSERVED HYPOTHETICAL PROTEIN TTHA1568 FROM THERMUS THERMOPHILUS HB8 (CYS11 MODIFIED WITH BETA-MERCAPTOETHANOL)
    4 2nxo 0.2896 3.318 PROTEIN SCO4506 FROM STREPTOMYCES COELICOLOR, PFAM DUF178
    5 2i48 0.2807 2.643 BICARBONATE TRANSPORT PROTEIN CMPA FROM SYNECHOCYSTIS SP. PCC 6803 IN COMPLEX WITH CARBONIC ACID
    6 2i49 0.2789 2.771 APO FORM OF BICARBONATE TRANSPORT PROTEIN CMPA FROM SYNECHOCYSTIS SP. PCC 6803
    7 2i4c 0.2744 2.747 BICARBONATE TRANSPORT PROTEIN CMPA FROM SYNECHOCYSTIS SP. PCC 6803 IN COMPLEX WITH BICARBONATE AND CALCIUM
    8 1xs5 0.2722 2.961 THE CRYSTAL STRUCTURE OF LIPOPROTEIN TP32 FROM TREPONEMA PALLIDUM
    9 2g29 0.261 2.867 THE PERIPLASMIC NITRATE-BINDING PROTEIN NRTA FROM SYNECHOCYSTIS PCC 6803
    10 2i6e 0.2567 3.755 PROTEIN DR0370 FROM DEINOCOCCUS RADIODURANS, PFAM DUF178

     

    Superposition of 3hn0 with structures 2i4b (bicarbonate transporter), 3efr (alkanesulfonate binding protein), and 2g29 (nitrate transporter) from the Dali and SSM results show that 3hn0 adopts a very similar structure to the others (Figure 3), with 3hn0 being most similar to 3efr.  Compared to 2i4b and 2g29, 3hn0 lacks several of the helices that are located at the periphery of the other two structures.

     

    Figure 3.  Superposition of 3hn0 (yellow) with 2i4b (blue), 3efr (green), and 2g29 (red).

    GS13941A-superpose.png

    While the overall structures are similar, a comparison of the substrate-binding sites (which is located at the cleft formed between the two globular domains), reveals little similarity between the corresponding residues.  What 3hn0 could bind, therefore, remains to be determined (1 molecule of phosphate per dimer is revealed in the crystal structure, around residue Arg-291).  The residues in 3hn0 which may constitute the substrate-binding site, based on sequence conservation, include Leu-31, Ser-35, Pro-80, Ile-82, Tyr-106, Thr-126, Pro-127, Pro-171, Gln-202, and Thr-203 (Figure 4.)

     

    Figure 4.  Putative binding site in 3hn0 structure.  A number of residues in this region are highly conserved.

    GS13941A-consurf-activesite.png

    consurf_legend.png

     

    References:

    The structure of a cyanobacterial bicarbonate transport protein, CmpA.  Koropatkin NM, Koppenaal DW, Pakrasi HB, Smith TJ.  J Biol Chem. 2007 Jan 26;282(4):2606-14.

    The ABC transporter structure and mechanism: perspectives on recent research.  Jones PM, George AM. Cell Mol Life Sci. 2004 Mar;61(6):682-99. Review.

    Structure, function, and evolution of bacterial ATP-binding cassette systems.  Davidson AL, Dassa E, Orelle C, Chen J. Microbiol Mol Biol Rev. 2008 Jun;72(2):317-64, table of contents. Review.

    ABC transporters: the power to change.  Rees DC, Johnson E, Lewinson O.  Nat Rev Mol Cell Biol. 2009 Mar;10(3):218-27. Review.

    Ligand Summary

    Reviews

    References

     

    No references found.

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