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The Open Protein Structure Annotation Network
PDB Keyword
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3hx8

    Title Crystal structure of putative ketosteroid isomerase (NP_103587.1) from MESORHIZOBIUM LOTI at 1.45 A resolution. To be published
    Site JCSG
    PDB Id 3hx8 Target Id 396313
    Molecular Characteristics
    Source Mesorhizobium loti maff303099
    Alias Ids TPS25899,NP_103587.1, 3.10.450.50, 327654 Molecular Weight 13925.84 Da.
    Residues 128 Isoelectric Point 5.12
    Sequence qsakeaieaanadfvkaynskdaagvaskymddaaafppdmarvdgrqniqklwqgamdmgiselkltt ldvqesgdfafesgsfslkapgkdsklvdaagkyvvvwrkgqdggwklyrdiwnsdpak
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.45 Rfree 0.186
    Matthews' coefficent 2.25 Rfactor 0.147
    Waters 637 Solvent Content 45.25

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hx8
    1. High_performance prediction of functional residues in proteins with machine learning and computed input features
    S Somarowthu, H Yang, DGC Hildebrand - , 2011 - Wiley Online Library
     

    Protein Summary

    Gene Mlr2180 from the nitrogen-fixing symbiotic bacterium Mesorhizobium loti encodes the protein NP_103587.1 which belongs to the NTF2-like superfamily. A sequence search at PFAM server does not return any definitive PFAM family.

    Note from PFAM: This is now in family SnoaL_2 PF12680.

     

    Similarly, a BLAST search returns a few weak hits, shown below.

                                                                                                 Score    E
    Sequences producing significant alignments:                      (bits) Value

    ref|NP_103587.1| hypothetical protein mlr2180 [Mesorhizobium lot...   278   1e-73
    ref|YP_001771499.1| hypothetical protein M446_4734 [Methylobacte...    89   1e-16
    ref|ZP_01223041.1| hypothetical protein P3TCK_18950 [Photobacter...    76   8e-13
    ref|ZP_01253171.1| hypothetical protein P700755_05979 [Psychrofl...    72   1e-11
    gb|EDY83942.1| hypothetical protein VDG1235_3569 [Verrucomicrobi...    66   9e-10
    gb|EED30413.1| putative beta-lactamase [gamma proteobacterium NO...    65   1e-09
    ref|ZP_01252034.1| hypothetical protein P700755_12232 [Psychrofl...    65   1e-09
    ref|XP_002208392.1| hypothetical protein BRAFLDRAFT_119600 [Bran...    64   6e-09
    ref|ZP_01102457.1| conserved hypothetical protein [gamma proteob...    63   8e-09
    ref|XP_001667023.1| Hypothetical protein CBG16427 [Caenorhabditi...    61   3e-08
    ref|ZP_01691089.1| conserved hypothetical protein [Microscilla m...    60   5e-08
    pir||T15990 hypothetical protein F09E10.7 - Caenorhabditis elegans     60   7e-08
    ref|YP_465495.1| hypothetical protein Adeh_2288 [Anaeromyxobacte...    57   3e-07
    ref|XP_001898163.1| hypothetical protein Bm1_33585 [Brugia malay...    57   6e-07
    ref|YP_546465.1| putative signal peptide protein [Methylobacillu...    55   1e-06
    ref|NP_001024545.1| hypothetical protein F09E10.7 [Caenorhabditi...    55   2e-06
    ref|XP_002208390.1| hypothetical protein BRAFLDRAFT_70928 [Branc...    54   4e-06

     

    However, a structure homolog search at DALI and SSM server finds several proteins with similar structures, see the tables below.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3d9r 18.2 2.2 128 132 19 KETOSTEROID ISOMERASE-LIKE PROTEIN
    2 2chc 17.7 2.4 123 159 18 PROTEIN RV3472
    3 3b7c 16.9 1.9 116 121 16 UNCHARACTERIZED PROTEIN
    4 3cu3 16.8 2.4 122 162 19 DOMAIN OF UNKNOWN FUNCTION WITH A CYSTATIN-LIKE
    5 2rgq 16.7 2.4 120 133 16 DOMAIN OF UNKNOWN FUNCTION WITH A CYSTATIN-LIKE
    6 3b8l 16.6 2.5 125 143 21 UNCHARACTERIZED PROTEIN
    7 3gzr 16.5 2.2 126 142 13 UNCHARACTERIZED PROTEIN WITH A NTF2-LIKE FOLD
    8 3ef8 16.4 2.4 124 149 16 PUTATIVE SCYALONE DEHYDRATASE
    9 2rfr 16.4 2.7 125 154 18 UNCHARACTERIZED PROTEIN
    10 3h51 16.3 2.8 125 140 18 PUTATIVE CALCIUM/CALMODULIN DEPENDENT PROTEIN
    SSM Structural Homologs
    N PDB Q-score RMSD TITLE
    1 3d9r 0.6767 1.816 KETOSTEROID ISOMERASE-LIKE PROTEIN (YP_049581.1) FROM ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 AT 2.40 A RESOLUTION
    2 1qma 0.589 1.932 NUCLEAR TRANSPORT FACTOR 2 (NTF2) W7A MUTANT
    3 2rgq 0.5873 1.705 DOMAIN OF UNKNOWN FUNCTION WITH A CYSTATIN-LIKE FOLD (ZP_00111510.1) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.80 A RESOLUTION
    4 2r4i 0.5836 1.954 NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (YP_678039.1) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 1.60 A RESOLUTION
    5 3gzr 0.5589 1.915 DOMAIN OF UNKNOWN FUNCTION WITH A NTF2- LIKE FOLD (NP_421374.1) FROM CAULOBACTER CRESCENTUS AT 1.40 A RESOLUTION
    6 3b8l 0.5588 1.745 NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (YP_001165924.1) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 AT 1.75 A RESOLUTION
    7 1oh0 0.5574 1.792 KETOSTEROID ISOMERASE COMPLEXED WITH EQUILENIN
    8 3gwr 0.5571 1.828 PUTATIVE CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ASSOCIATION DOMAIN (YP_315894.1) FROM THIOBACILLUS DENITRIFICANS ATCC 25259 AT 2.00 A RESOLUTION
    9 1w00 0.5514 1.794 MUTANT ENZYME D103L OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA BIOTYPE B
    10 3h51 0.5487 1.990 PUTATIVE CALCIUM/CALMODULIN DEPENDENT PROTEIN KINASE II ASSOCIATION DOMAIN (NP_636218.1) FROM XANTHOMONAS CAMPESTRIS AT 1.70 A RESOLUTION

     Of these, 11 structures (2r4i 2rfr 2rgq 3b7c 3b8l 3cu3 3d9r 3ef8 3gwr 3gzr 3h51) have been determined at JCSG.

     

    SCOP classifies 3hx8 inside the NTF2-like superfamily. The protein adopts a simple alpha+beta fold forming a barrel shape, shown below.

    PX15605B_mon.png

    The size exclusion chromatography and crystal packing analysis suggest that the protein is a dimer in solution. Two views of the dimerization mode is shown below.

    PX15605B_dimer.pngPX15605B_dimer2.png

    There are four monomers in the crystallographic asu. Each monomer has an unknown ligand (UNL) bound in the core of the protein. The figure below shows the UNL (in spherical representation) enveloped in an unbiased (DM) density.

    PX15605B_unl.png

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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