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1o5u

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

    Title Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution. Proteins 56 615-618 2004
    Site JCSG
    PDB Id 1o5u Target Id 282978
    Related PDB Ids 2k9z 
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1262,TM1112, 2.60.120.10, 282123 Molecular Weight 10756.93 Da.
    Residues 89 Isoelectric Point 5.50
    Sequence mevkiekptpeklkelsvekwpiwekevsefdwyydtnetcyilegkvevttedgkkyviekgdlvtfp kglrcrwkvlepvrkhynlf
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.83 Rfree 0.22239
    Matthews' coefficent 2.48 Rfactor 0.17011
    Waters 282 Solvent Content 49.95

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1o5u
    1. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
    Y Shen, F Delaglio, G Cornilescu, A Bax - Journal of biomolecular NMR, 2009 - Springer
     
    2. The importance of alignment accuracy for molecular replacement
    R Schwarzenbacher, A Godzik - Section D: Biological , 2004 - scripts.iucr.org
     
    3. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    SB Conners, EF Mongodin, MR Johnson - FEMS microbiology , 2006 - Wiley Online Library
     
    4. The JCSG MR pipeline: optimized alignments, multiple models and parallel searches
    R Schwarzenbacher, A Godzik - Section D: Biological , 2007 - scripts.iucr.org
     
    5. Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 resolution
    Q Xu, R Schwarzenbacher, S Sri Krishna - Proteins: Structure, , 2006 - Wiley Online Library
     
    6. Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins
    R Page, AM Deacon, SA Lesley - Journal of structural and , 2005 - Springer
     
    7. High-throughput protein production for X-ray crystallography and use of size exclusion chromatography to validate or refute computational biological unit predictions
    D McMullan, JM Canaves, K Quijano - Journal of structural and , 2005 - Springer
     
    8. Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 resolution
    D McMullan, R Schwarzenbacher - Proteins: Structure, , 2004 - Wiley Online Library
     
    9. Comparison of NMR and crystal structures for the proteins TM1112 and TM1367
    B Mohanty, P Serrano, B Pedrini - Section F: Structural , 2010 - scripts.iucr.org
     
    10. Towards automated structure-based NMR assignment
    R Jang, X Gao, M Li - 2009 - Citeseer
     
    11. Towards automated structure-based NMR resonance assignment
    R Jang, X Gao, M Li - Research in Computational Molecular Biology, 2010 - Springer
     
    12. Integer Programming Model for Automated Structure-based NMR Assignment
    R Jang, X Gao, M Li - 2009 - cs.uwaterloo.ca
     
    13. Carbohydrate utilization pathway analysis in the hyperthermophile Thermotoga maritima
    SB Conners - 2006 - repository.lib.ncsu.edu
     
    14. An Evaluation of the Impact of Side Chain Positioning on the Accuracy of Discrete Models of Protein Structures
    M Bugalho, A Oliveira - Advances in Bioinformatics and Computational , 2008 - Springer
     
    15. Constant Time Clash Detection in Protein Folding
    MMF Bugalho, AL Oliveira - Journal of Bioinformatics and , 2009 - inesc-id.pt
     
    16. Optimizations of protein force fields
    Y Sakae, Y Okamoto - Arxiv preprint arXiv:1208.6150, 2012 - arxiv.org
     
    17. An efficient clash detection method for molecular structures applications
    MMF Bugalho, AL Oliveira - 2007 - Citeseer
     

    Protein Summary

    The TM1112 gene of Thermotoga maritima encodes the conserved hypothetical protein NP_228918 (Pfam05899; DUF861) with unknown function [Ref]. This family consists of several bacterial and plant proteins. TM1112 has similar phylogenetic cooccurrence (string.embl.de) as TM1189 (putative KAP NTPase), indicating that functions of both proteins may be interdependent.

    The 1o5u structure has a double-stranded beta-helix fold (SCOP sunid:51181), where one turn of helix is made by two pairs of antiparallel strands linked with short turns that has appearance of a sandwich of distinct architecture and jelly-roll topology. 1o5u belongs to the superfamily of RmlC-like cupins (SCOP sunid:51182), and has its own family. DALI top hits are with the DUF1255 protein 3eo6 (Z=11) and the uncharacterized protein 3bcw (Z=10).

    1o5u has a large number of similar (Z<8) structures (PDB:2b8m, PDB:1yhf, PDB:1vj2, PDB:1vr3, PDB:2f4p, PDB:2fqp, PDB:2atf, PDB:1v70, PDB:1zz6, PDB:1m4o, PDB:1xja, PDB:1qwr, PDB:1lr5, PDB:1yfu, PDB:1od5, PDB:1j3p, PDB:1sef, PDB:1y9q, PDB:1ey2, PDB:1sq4, PDB:1zvf, PDB:1uik, PDB:1o4t, PDB:1sfn, PDB:1rc6, PDB:1zx5, PDB:1vrb, PDB:1j58, PDB:2gm6, PDB:1tq5, PDB:2h0v, PDB:1ipj, PDB:2cv6, PDB:1fi2, PDB:2cau, PDB:1fxz, PDB:1x7n). However it is unknown what functional implications, if any, can be obtained on the basis of structural similarity to those structures.

    Analysis of the crystallographic packing of 1o5u using the PQS server {Henrick, 1998 #73} indicates that a monomer is the biologically relevant form. The alpha-helix 1 and 2 of 1o5u prevent dimerization of this protein in a way commonly observed for other proteins with cupin fold.

    Ligand Summary

    One of the unknown ligands (UNL401) interacts with residues from chain A: Tyr35, Glu39, Cys41, Trp76. This ligand is covalently bound to Lys84 from chain A.
    The UNL401 is located in a cleft containing highly conserved Trp24, Glu39, and Tyr86.


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