The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of hypothetical protein (tm1410) from THERMOTOGA MARITIMA at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 2aam Target Id 358470
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1393,TM1410 Molecular Weight 34516.78 Da.
    Residues 294 Isoelectric Point 4.42
    Sequence wfmpfdnwlyqlqnadpveisssgfeiavidyskdgsesgeyspeeikimvdagvvpvayvnigqaedy rfywkeswytntpewlgeedpawpgnyfvkywynewkeivfsyldrvidqgfkgiyldridsfeywaqe gvisrrsaarkminfvleiaeyvrerkpdmliipqngenildfddgqlastvsgwavenlfylktiple enetksrleylirlnrkgkfilsvdyvddgsdsfenisrildyyekakrngcipyaarsdleldemnvi egiqppealkdyesrtyr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 2.20 Rfree 0.239
    Matthews' coefficent 6.43 Rfactor 0.216
    Waters 926 Solvent Content 80.71

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    Ligand Information


    Google Scholar output for 2aam
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    2. Biosynthesis of the Pseudomonas aeruginosa extracellular polysaccharides, alginate, Pel, and Psl
    MJ Franklin, DE Nivens, JT Weadge - Frontiers in , 2011 - ncbi.nlm.nih.gov
    3. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
    4. Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634
    CJ McCleverty, L Columbus, A Kreusch - Protein , 2008 - Wiley Online Library
    5. Sequence analysis of COG3868 and COG2342 families
    OO Stepuschenko, DG Naumoff - Regulat. Struct. Systems Biol., June 20 , 2010 - conf.nsc.ru
    6. Endo-_-1, 4-polygalactosaminidases and their homologs: Structure and evolution
    DG Naumoff, OO Stepuschenko - Molecular Biology, 2011 - Springer
    7. COG2342 is a family of hypothetical glycoside hydrolases
    D Naumoff, O Stepuschenko - Department of Bioengineering and , 2011 - lab6.iitp.ru

    Protein Summary

    The TM1410 gene from Thermotoga maritima encodes the NP_229211 protein from the DUF297 group (PF03537) with homologs found in all domains of life (eukaryotes, archaea, bacteria, viruses). FFAS identifies remote homology between this family and PF03644 (score -13.6) family of endo-beta-N-acetylglucosammidases (Glycosyl hydrolase 85), PF02638 (score -16.7) family of unknown function DUF187 and PF12138 (score -10.5) spherulation-specific family 4. Gene fusion analysis supports an outer membrane localization (fusion with fibronectin type III and bacterial cell adhesion related domains) with possible role in carbohydrate processing (fusion with polysaccharide deacetylase). Genome context analysis indicates a possible functional link (score 0.9)  between genes TM1410 and TM1405, coding for a lipopolysaccharide biosynthesis-related protein.

    SCOP classifies the 2aam structure in the alpha/beta class as a TIM barrel fold belonging to the (trans)glycosidase superfamily. DALI top hits are with the sucrose hydrolase 3czk (Z=15), the amylosucrase 1zs2 (Z=15), and the putative glucosidase YICI 2f2h (Z=15).

    Overall, structure, sequence and gene fusion support a role for this family as a glycosyl hydrolase. The Pseudomonas   homolog (PA3064) has been shown to function as an e Experimental work carried out on the Methanococcus jannaschii and Deinococcus radiodurans homologs (MJ1477 and DR_0705 respectively) indicate that they act as a cysteinyl tRNA synthetase both in vivo and in vitro [Ref]. However, this analysis has been contested [Ref] and is now widely regarded as incorrect. TM1410 assignment as Cysteinyl-tRNA synthetase (EC: has been used in T. maritima reconstruction (see the pathway box above) and has to be corrected (to be done).

    Closer study of genomic neighborhood (JCVI) indicates a separation between those genes (e.g. MJ1477, DR_0705) clustering with aminotransferases, tRNA/rRNA methyltransferases and other tRNA synthases and those (e.g. Saro_0530, Gmet_1962) clustering with membrane-related proteins (membrane fusion, type I secretion system, cadherin, putative lipoprotein and integral membrane proteins, glycosyl transferase, fibronectin type III). For T. maritima, eighty-one archaeal-like genes, ranging in size from 4-20kb, are clustered in 15 regions ofthe genome with conservation of gene order between T. maritima and Archaea in many of these regions suggesting that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea [Ref].



    To do: identify UNL ligand present in equivalent positions in each of the 6 chains chelated by the conserved side chains of residues Y98 and R99; check whether there is conservation of the helix shared by class I and II CysRS; carry out phylogenetic/sequence analysis to determine whether two distinct functional subfamilies can be identified

    Ligand Summary






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