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The Open Protein Structure Annotation Network
PDB Keyword
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3htv

    Title Crystal structure of D-allose kinase (NP_418508.1) from ESCHERICHIA COLI K12 at 1.95 A resolution. To be published
    Site JCSG
    PDB Id 3htv Target Id 394118
    Molecular Characteristics
    Source Escherichia coli k12
    Alias Ids TPS25773,NP_418508.1, _0079.001987_, 332725 Molecular Weight 33819.11 Da.
    Residues 309 Isoelectric Point 6.55
    Sequence mqkqhnvvagvdmgathirfclrtaegetlhcekkrtaeviapglvsgigemideqlrrfnarchglvm gfpalvskdkrtiistpnlpltaadlydladklentlncpvefsrdvnlqlswdvvenrltqqlvlaay lgtgmgfavwmngapwtgahgvagelghiplgdmtqhcacgnpgcletncsgmalrrwyeqqprnyplr dlfvhaenapfvqsllenaaraiatsinlfdpdavilgggvmdmpafpretlvamtqkylrrplphqvv rfiaasssdfngaqgaailahqrflpqfcakap
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.95 Rfree 0.241
    Matthews' coefficent 2.26 Rfactor 0.197
    Waters 139 Solvent Content 45.59

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3htv
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

    The protein NP_418508.1 is annotated as a putative NAGC-like transcriptional regulator protein. NP_418508.1 belongs to PFAM PF00480which consists of bacterial proteins including transcriptional repressors, sugar kinases and yet uncharacterised open reading frames, ROK (Repressor, ORF, Kinase).

    The protein is a mixed alpha+beta protein and consists of two domains as shown below.

    MH15503A.png    MH15503A_domains.png

    Rainbow colored from N- to C-terminus                                                        Domain view

     

    The protein most likely forms a dimer in solution with the following dimerization mode.

    MH15503A_dimer.png

     

    There are several sequence homologs of this protein as obtained from a BLAST search:

                                                                                                Score    E
    Sequences producing significant alignments:                      (bits) Value

    ref|NP_418508.1| D-allose kinase [Escherichia coli str. K-12 sub...   643   0.0
    ref|AP_004586.1| D-allose kinase [Escherichia coli str. K-12 sub...   640   0.0
    ref|YP_001726870.1| ROK family protein [Escherichia coli ATCC 87...   640   0.0
    ref|ZP_03030540.1| D-allose kinase [Escherichia coli B7A] >gi|19...   636   0.0
    ref|YP_002295657.1| D-allose kinase [Escherichia coli SE11] >gi|...   635   e-180
    ref|YP_672173.1| D-allose kinase [Escherichia coli 536] >gi|1911...   633   e-180
    ref|YP_002400593.1| D-allose kinase [Escherichia coli ED1a] >gi|...   630   e-179
    ref|YP_543619.1| D-allose kinase [Escherichia coli UTI89] >gi|11...   629   e-179
    ref|YP_002410379.1| D-allose kinase [Escherichia coli IAI39] >gi...   628   e-178
    ref|NP_756941.1| D-allose kinase [Escherichia coli CFT073] >gi|2...   627   e-178
    ref|YP_001746478.1| D-allose kinase (allokinase) [Escherichia co...   625   e-177
    ref|YP_002331866.1| D-allose kinase [Escherichia coli O127:H6 st...   623   e-177
    ref|YP_001455301.1| D-allose kinase [Citrobacter koseri ATCC BAA...   511   e-143
    ref|YP_002385295.1| D-allose kinase (Allokinase) [Escherichia fe...   459   e-127
    ref|ZP_00834431.1| COG1940: Transcriptional regulator/sugar kina...   415   e-114
    ref|ZP_03622996.1| ROK family protein [Tolumonas auensis DSM 918...   340   1e-91
    ref|YP_001783902.1| ROK family protein [Haemophilus somnus 2336]...   283   1e-74
    ref|YP_076168.1| D-allose kinase [Symbiobacterium thermophilum I...   199   2e-49
    ref|ZP_03653381.1| D-allose kinase [Clostridiales bacterium 1_7_...   191   1e-46
    ref|ZP_02026275.1| hypothetical protein EUBVEN_01531 [Eubacteriu...   184   7e-45
    ref|ZP_03653805.1| D-allose kinase [Clostridiales bacterium 1_7_...   151   7e-35
    ref|ZP_02918058.1| hypothetical protein BIFDEN_01357 [Bifidobact...   137   1e-30
    ref|YP_002250838.1| glucokinase [Dictyoglomus thermophilum H-6-1...   134   1e-29
    ref|YP_002353009.1| ROK family protein [Dictyoglomus turgidum DS...   126   3e-27
    ref|YP_001620526.1| ROK family glucose/fructose kinase [Acholepl...   116   3e-24
     

    Simlarly, there are many structural homologs as well.

    DALI Structural Homologs

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2qm1 25.3 2.8 267 324 25 GLUCOKINASE
    2 2hoe 24.7 3.1 264 354 18 N-ACETYLGLUCOSAMINE KINASE
    3 2gup 23.8 2.9 257 289 21 ROK FAMILY PROTEIN
    4 2ap1 22.9 3.3 259 305 23 PUTATIVE REGULATOR PROTEIN
    5 2aa4 22.9 3.0 254 289 20 PUTATIVE N-ACETYLMANNOSAMINE KINASE
    6 3eo3 22.1 2.8 241 283 18 BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-
    7 3epq 22.0 2.6 247 294 21 PUTATIVE FRUCTOKINASE
    8 1xc3 21.8 2.8 249 295 19 PUTATIVE FRUCTOKINASE
    9 1z05 21.7 3.2 267 396 19 TRANSCRIPTIONAL REGULATOR, ROK FAMILY
    10 1z6r 21.5 3.2 265 382 16 MLC PROTEIN

     

    A superposition of these structures is shown below.

    MH15503A_all.png

    Color Scheme: NP_418508.1 (green), 1xc3 (cyan), 1z05 (lightmagenta), 1z6r (yellow), 2aa4 (salmon), 2ap1 (lightgrey), 2gup (slate), 2hoe (orange), 2qm1 (lime), 3eo3 (deepteal), 3epq (hotpink).

    Of these, 1z05 (lightmagenta), 1z6r (yellow), and 2hoe (orange) have an extra domain as compared to the rest of these proteins.
     

     

    The sequence and structural homolog results suggest that the protein could have a kinase/transcriptional regulator activity.

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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