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1vj2

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

    Title Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution. Proteins 56 611-614 2004
    Site JCSG
    PDB Id 1vj2 Target Id 283317
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1289,TM1459, 2.60.120.10, 84720, 84829 Molecular Weight 13108.44 Da.
    Residues 114 Isoelectric Point 5.60
    Sequence milkraydvtpqkistdkvrgvrkrvliglkdapnfvmrlftvepgglidrhshpweheifvlkgkltv lkeqgeetveegfyifvepneihgfrndtdseveflclipkegge
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.65 Rfree 0.24859
    Matthews' coefficent 2.71 Rfactor 0.20817
    Waters 169 Solvent Content 54.20

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vj2
    1. The importance of alignment accuracy for molecular replacement
    R Schwarzenbacher, A Godzik - Section D: Biological , 2004 - scripts.iucr.org
     
    2. Crystal structure of mammalian cysteine dioxygenase
    CR Simmons, Q Liu, Q Huang, Q Hao - Journal of Biological , 2006 - ASBMB
     
    3. Microbial metalloproteomes are largely uncharacterized
    A Cvetkovic, AL Menon, MP Thorgersen, JW Scott - Nature, 2010 - nature.com
     
    4. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    SB Conners, EF Mongodin, MR Johnson - FEMS microbiology , 2006 - Wiley Online Library
     
    5. An iterative knowledge_based scoring function for proteinprotein recognition
    SY Huang, X Zou - Proteins: Structure, Function, and , 2008 - Wiley Online Library
     
    6. Structure and reactivity of hydroxypropylphosphonic acid epoxidase in fosfomycin biosynthesis by a cation-and flavin-dependent mechanism
    K McLuskey, S Cameron - Proceedings of the , 2005 - National Acad Sciences
     
    7. The JCSG MR pipeline: optimized alignments, multiple models and parallel searches
    R Schwarzenbacher, A Godzik - Section D: Biological , 2007 - scripts.iucr.org
     
    8. Crystal structure of XC5357 from Xanthomonas campestris: A putative tetracenomycin polyketide synthesis protein adopting a novel cupin subfamily structure
    KH Chin, CC Chou, AHJ Wang - : Structure, Function, and , 2006 - Wiley Online Library
     
    9. Cupin: A candidate molecular structure for the Nep1-like protein family
    A Cechin, M Sinigaglia, N Lemke - BMC plant , 2008 - biomedcentral.com
     
    10. The crystal structure of 5_keto_4_deoxyuronate isomerase from Escherichia coli
    RL Crowther, MM Georgiadis - Proteins: Structure, Function, , 2005 - Wiley Online Library
     
    11. Crystallization and preliminary X-ray diffraction studies on the bicupin YwfC from Bacillus subtilis
    M Rajavel, B Gopal - Section F: Structural Biology and Crystallization , 2006 - scripts.iucr.org
     
    12. Carbohydrate utilization pathway analysis in the hyperthermophile Thermotoga maritima
    SB Conners - 2006 - repository.lib.ncsu.edu
     

    Protein Summary


    Gene TM1459 from Thermotoga Maritima encodes the protein NP_229258 whose structure (1vj2) is the first representative of a novel subfamily of cupins (PF07883) containing manganese that is coordinated by four histidines (His52, His54, His58, and His92) [Ref].

    TM1459 has similar phylogenetic cooccurrence (string.embl.de) as TM0243 (a member of SAM radical superfamily).

    1vj2 classifies inside the SCOP all beta class, RmlC-like cupins superfamily, TM1459 family. DALI top hits are with the RemF polyketide cyclase PDB:3ht1 (Z=17), a putative oxalate decarboxylase PDB:1o4t (Z=16), and the cupin-2 protein PDB:2pfw (Z=15). RemF also has significant (36%) sequence homology to TM1459 but shows a two-helix C-terminal extension of unknown function. Despite very similar coordination chemistry and geometry, the metal in RemF was identified as zinc or nickel, depending on the crystallization conditions [Ref].

    Analysis of the crystallographic packing of 1vj2 using the PQS server {Henrick, 1998 #73} indicates that a dimer is the biologically relevant form. The N-terminal beta-strand is part of the beta-sheet of the opposite subunit, suggesting a bona fide dimer.

    PDB entry 1o5n was replaced by 1vj2

    Ligand Summary



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