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3d4o

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

    Title Crystal structure of dipicolinate synthase subunit A (NP_243269.1) from BACILLUS HALODURANS at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 3d4o Target Id 379058
    Molecular Characteristics
    Source Bacillus halodurans c-125
    Alias Ids TPS1731,NP_243269.1 Molecular Weight 31525.02 Da.
    Residues 292 Isoelectric Point 6.10
    Sequence mltgkhvviiggdarqleiirklstfdakislvgfdqlddgfigvtkmridevdwntvdaillpisgtn eagkvdtifsnesivlteemiektpnhcvvysgisntylnqcmkktnrtlvklmerddiaiynsiptae gtimmaiqhtdftihganvavlglgrvgmsvarkfaalgakvkvgaresdllariaemgmepfhiskaa qelrdvdvcintipalvvtanvlaempshtfvidlaskpggtdfryaekrgikallvpglpgivapkta griladvlvkllaeps
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.10 Rfree 0.240
    Matthews' coefficent 2.47 Rfactor 0.189
    Waters 645 Solvent Content 50.26

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3d4o
    1. FAMSD: A Powerful Protein Modeling Platform that Combines Alignment Methods, Homology Modeling, 3D Structure Quality Estimation and Molecular
    K Kanou, M Iwadate, T Hirata, G Terashi - Chemical & , 2009 - bioinf.jku.at
     

    Protein Summary

    This protein is annotated as dipicolinate synthase subunit A (gi|15614966|ref|NP_243269.1) from Bacillus halodurans. The protein belongs to the PFAM PF01262 which is characterized as Alanine dehydrogenase/PNT, C-terminal domain. The structure consists of two almost identical domains. Each domain has a five stranded sheet flanked by three helices on both sides (Fig 1)
    FN12445A_monomer.pngFN12445A_A_twodomains.png
                                               A                                                                                   B
    Fig 1: A. Monomer structure consists of two identical domains. B. Supeposing one domain onto the other (in chain A) illustrates the similarity between domains

    FN12445A_tetramer.png

    Fig 2: There are four monomers in the asu


    While chains A/B and C/D are identical in structure within each pair, they show significant differences when compared across the dimmer pair (A/C and B/D) (Fig 3).
    FN12445A_dimers_AB.pngFN12445A_dimers_AC.pngFN12445A_AonCwith2ndDomainSuperposed.png
                    A                                B                                   C

    Fig 3: Two kinds of monomers. A. Chain A and B superpose well on each other (green and cyan) as do chain C and D (yellow and magenta). B. But chain A and C (green and yellow) and chains B and D (green and magenta) do not superpose that well. C. Using the second domain of chain A to superpose chain A onto chain C illustrates a domain motion between the monomers.

    This is not a novel structure as the structure of the same protein from Bacillus subtilis is known (pdb id 2rir). The proteins are identical in structure (Fig 4). The protein 2rir has a ligand (NAP) bound to it, but the corresponding site in this target is empty.
    FN12445A_2rir.png

    Fig 4: This target (green) superposed on 2rir (magenta) which is the homologous protein from Bacillus subtilis.

     Additional structural homologs of this proteins are listed in FFAS results (2vhv, 1f8q,2eez).

    Ligand Summary



    References

    1. Azevedo RA, Lea PJ; , Amino Acids 2001;20:261-279.: Lysine metabolism in higher plants.  PUBMED:11354603
    2. Studley WK, Yamaguchi M, Hatefi Y, Saier MH Jr. Phylogenetic analyses of proton-translocating transhydrogenases.Microb Comp Genomics. 1999;4(3):173-86.PMID: 10587945
    3. Maringanti S, Imlay JA. An intracellular iron chelator pleiotropically suppresses enzymatic and growth defects of superoxide dismutase-deficient Escherichia coli. J Bacteriol. 1999 Jun;181(12):3792-802. PMID: 10368155
    4. Chen NY, Jiang SQ, Klein DA, Paulus H. Organization and nucleotide sequence of the Bacillus subtilis diaminopimelate operon, a cluster of genes encoding the first three enzymes of diaminopimelate synthesis and dipicolinate synthase. J Biol Chem. 1993 May 5;268(13):9448-65. PMID: 8098035
    5. Laber B, Gomis-Rüth FX, Romão MJ, Huber R. Escherichia coli dihydrodipicolinate synthase. Identification of the active site and crystallization. Biochem J. 1992 Dec 1;288 ( Pt 2):691-5. PMID: 1463470
    6. Roten CA, Brandt C, Karamata D. Genes involved in meso-diaminopimelate synthesis in Bacillus subtilis: identification of the gene encoding aspartokinase I. J Gen Microbiol. 1991 Apr;137(4):951-62. PMID: 1906928

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