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3iv7

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

    Title Crystal structure of Iron-containing alcohol dehydrogenase (NP_602249.1) from Corynebacterium glutamicum ATCC 13032 KITASATO at 2.07 A resolution. To be published
    Site JCSG
    PDB Id 3iv7 Target Id 394438
    Molecular Characteristics
    Source Corynebacterium glutamicum atcc 13032
    Alias Ids TPS25798,NP_602249.1, _0056.000797_ Molecular Weight 38296.39 Da.
    Residues 363 Isoelectric Point 5.32
    Sequence mnnslafnhdtlpqkvmfgygkssaflkqeverrgsakvmviageremsiahkvaseievaiwhdevvm hvpievaeraravatdneidllvcvgggstiglakaiamttalpivaipttyagseatnvwglteaark ttgvdlkvlpetviydseltmslpvemsvasglnglahcidslwgpnadpinavlaaegiralnqglpk ivanphsiegrdealygaylaavsfasagsglhhkichtlggtfnlphaqthatvlpyvlafnagdape aerraaaafgtdtaleglqrlrlsvnapkrlsdygfeasgiaeavdvtlekvpannprpvtrenlsrll eaalngedpavlsavlsn
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.07 Rfree 0.221
    Matthews' coefficent 2.40 Rfactor 0.171
    Waters 398 Solvent Content 48.67

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3iv7

    Protein Summary

    Target ID 394438 belongs to theFe-ADH (PF00465)Pfam A  group. Over 22 structures from this Pfam group have been determined, and include alcohol dehydrogenases (Fe-dependent), propanediol oxidoreductase,NADH-dependent butanol dehydrogenases, acetaldehyde dehydrogenase, and E. coli hypothetical protein yiaY.

    An NCBI BLAST search reveals that the amino acid sequence of target id 394438 described here shows ~80% sequence identity with sequences from Rhodococcus opacus B4 and Arthrobacter sp. JS443 that have been functionally annotated as a maleylacetetae reductase (EC 1.3.1.32), and suggests that target ID 394438 functions as a maleylacetate reductase. This  enzyme catalyzed the NAD(P)H dependent reduction of 2-maleylacetate to 3-oxoadipate, and this enzyme is required for the degradation of phenols, resorcinol, and environmental contaminats such as chlorobenzoate. A search of the Pubmed using the keywords "maleylacetate reductase" and "Corynebacterium" returns one citation. (see PubMed ID 16963551) entitled "Genetic Characterization of the  Resorcinol Catabolic Pathway in Corynebacterium glutamicum."  This citation describes functional investigations that two genes, NCgl1112 and NCgl2952 code for maleylacetate reductase. A paiwise BLAST search shows that the amino acid sequence encoded by NCgl2952 is 100% identical with that of target ID 394438. Therefore, target ID 394438 described here is a maleylacetate reductase. The structure determination of a related protein is now underway at JCSG.  This protein , Target ID 394332, is from Ralstonia eutropha jmp134.

    Shown below is a ribbon reprensentation of the structure of target ID 394438 color-coded so that the N-terminal end is in blue and the

    monomer.png

    C-terminal end is in red.  The structure was determined to a resolution of 2.06 Angstroms using Se-Single wavelength anomalous dispersion (SAD). The structure is comprised primarily of two domains and belongs to the dehydroquinate-like synthease SCOP superfamily of protein structures.  The N-terminal domain forms a Rossman-like fold and the C-terminal domain consists of a cylindrical array of alpha-helices.dimer.png

     

    The crystal structure indicates a dimer is the biologically-relevant oligmerization state, and static light scattering measurements provide supporting evidence that a dimer is a significant oligomerization state in solution. The ribbon representation shows the dimeric form of the structure of target ID 394438 with individual monomers represented in green and blue. The N-terminal ends one from each monomer closely interact to form an inter-subunit beta-sheet that stabilizes the dimer.

    A search of the PDB with the DALI server using the coordinates of target ID 394438 shows structural similarity with the following entries

    PDB ID Z-score rmsd (Ang) lalign

    %seq

    id

    Description
    3bfj 45.5 1.8 342 25 1,3-propanediol oxidoreductase from Klebsiella pneumoniae (EC 1.1.1.202)
    1rrm 43.3 2.2 342 25 Lactaldehyde reductase from E. Coli  (EC 1.1.1.77)
    2bl4 42.7 2.1 339  28 

    Iron-Dependent Group III Dehydrogenase that Interconverts L-Lactaldehyde and L-1,2-Propanediol in Escherichia Coli.(EC 1.1.1.77)

    1vhd 38.3 2.5 333  23 

    iron containing alcohol dehydrogenase from Thermotoga maritima

    1o2d   37.8  2.6 330  23 Alcohol dehydrogenase, iron-containing (TM0920) from Thermotoga maritima at 1.30 A resolution (EC 1.1.1.1)
    1vlj 35.9 3.1 343  23 NADH-dependent butanol dehydrogenase A (TM0820) from Thermotoga maritima at 1.78 A resolution
    1oj7 35.1 3.0 336 21  STRUCTURAL GENOMICS, UNKNOWN FUNCTION CRYSTAL STRUCTURE OF E. COLI K-12 YQHD
    1jq5 34.9 2.5 328  19

    Bacillus Stearothermophilus Glycerol dehydrogenase complex with NAD+

    (EC 1.1.1.6)

    1kq3 33.2 2.7 327  19 Glycerol Dehydrogenase (TM0423) from Thermotoga maritima at 1.5 A Resolution (EC 1.1.1.6)
    1ta9  32.0 2.7  325 15 glycerol dehydrogenase from Schizosaccharomyces pombe

     

     Quite recently, on May 26, 2009, the Midwest Center for Structural Genomics, deposited the structure of maleylacetate reductase from Agrobacterium tumefaciens str C58. PDB ID 3hl0, representing the first crystal structure of a maleylacetate reductase deposited. Previously, a group from Kyoto University reported in the crystallization and x-ray structure deterination of maleylacetate reductase from Rhizobium sp. strain MTP-10005 (PubMed ID 18678945) .

     The image below shows the similarity between the structures of maleylacetate reductase from Corynebacterium (target id 399438)(blue) and Agrobacterium (PDB ID 3hl0) (yellow). A bound NAD  cofactor from the crystal structure of the Agrobacterium enzyme is shown in red sticks. The location of the bound NAD is in the vicinity of the active site on both proteins.

     

    ovelap_with_3hl0.png

     A pairwise DALI comparison of the two structures shows that 338 residues are aligned with an rmsd overlap of 1.5 Angstrom and a sequence identity of 39%.

     

    0-0-1245781564-esp.bmp 

     

     

     

     

     

     

     

     

     

     

     

     Shown here is an alignment of the amino acid sequences for targetID 399438 and PDB ID 3hl0.

     

     

     

     

     

     

    During the refinement of target ID 394438 extra electron density (blue) was observed on one of the subunits in the crystallographic asymmetric unit.. Based on a comparison with the related structure, PDB ID 3hl0, this electron density is believed to be  associated with the active site. An NAD cofactor was modeled into the density with a partial occupancy of 50%.

    NAD_density.bmp 

     

     

     

     

     

     Shown below is a superpositioning of the structures surrounding the active site in  target ID 399438 (green rendering) and PDB ID 3hl0 ( blue rendering). The numbered residues belong to target ID 399438. Several residues surrounding the NAD are conserved, including a cluster of three His residues and an Asn residue near the nicotinamide moiety of the NAD.

     

     

    NAD_binding_site.bmp

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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