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The Open Protein Structure Annotation Network
PDB Keyword
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1z9t

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

    Title Crystal structure of Hypothetical UPF0124 protein yfiH (np_417084.1) from Escherichia coli K12 at 1.54 A resolution. To be published
    Site JCSG
    PDB Id 1z9t Target Id 358298
    Molecular Characteristics
    Source Escherichia coli k12
    Alias Ids TPS1388,NP_417084.1 Molecular Weight 26337.48 Da.
    Residues 243 Isoelectric Point 6.22
    Sequence msklivpqwpqpkgvaacsstriggvslppydslnlgahcgdnpdhveenrkrlfaagnlpskpvwleq vhgkdvlkltgepyaskradasysntpgtvcavmtadclpvlfcnragtevaaahagwrglcagvleet vscfadnpenilawlgpaigprafevggevreafmavdakasaafiqhgdkyladiyqlarqrlanvgv eqifggdrctytenetffsyrrdkttgrmasfiwli
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.54 Rfree 0.172
    Matthews' coefficent 2.47 Rfactor 0.142
    Waters 218 Solvent Content 49.84

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The gene yfiH from Escherichia coli k12 encodes the NP_417084.1 protein, a putative multicopper polyphenol oxidase (laccase) PF02578 EC:1.10.3.2.  NP_417084 shows the conserved motif  H-71, 105-ADCLP-109, H-124 that includes the putative catalytic histidines capable of binding copper. Alternative name for this enzyme is urishiol oxidase. Its genome context indicates a possible functional link (score 0.96) with rluD, a ribosomal large subunit pseudouridine synthase D.  

    The 1z9t structure belongs to the class of alpha and beta (a+b) proteins and reveals a CNF1/YfiH-like putative cysteine hydrolases fold type SCOP64437.  According to DALI, 1z9t is structurally similar to the NMB0706 protein 1rv9 (Z=38), the protein CC_0490 (DUF152) from Caulobacter crescentus 1XFJ (Z=33), and the YLMD protein 1t8h (Z=32).

    Laccases act on phenols and similar molecules, performing a one-electron oxidations, which remain poorly defined. Example: 4 benzenediol + O(2) <=> 4 benzosemiquinone + 2 H(2)O.  It is proposed that laccases play a role in the formation of lignin by promoting the oxidative coupling of lignols, a family of naturally occurring phenols. The enzymatically active form of the enzyme can be a dimer or a trimer. 

    Ligand Summary



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