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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS THII, A TRNA-MODIFYING ENZYME CONTAINING THE PREDICTED RNA-BINDING THUMP DOMAIN
 
Authors :  D. G. Waterman, M. Ortiz-Lombardia, M. J. Fogg, E. V. Koonin, A. A. Ants
Date :  01 Nov 05  (Deposition) - 30 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rna-Binding Protein, Rna Binding Protein, Trna Modification, 4-Thiouridine Synthase, Ferredoxin-Like Domain, Thump Domain, Pp-Loop Pyrophosphatase Domain, Thiamine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. G. Waterman, M. Ortiz-Lombardia, M. J. Fogg, E. V. Koonin, A. A. Antson
Crystal Structure Of Bacillus Anthracis Thii, A Trna-Modifying Enzyme Containing The Predicted Rna- Binding Thump Domain.
J. Mol. Biol. V. 356 97 2006
PubMed-ID: 16343540  |  Reference-DOI: 10.1016/J.JMB.2005.11.013

(-) Compounds

Molecule 1 - PROBABLE THIAMINE BIOSYNTHESIS PROTEIN THII
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: YSBLIC (MODIFIED PET-28A)
    Expression System Strain: BL21/B834
    Expression System Taxid: 511693
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 198094
    Other Details: GENOMIC DNA PROVIDED BY PROFESSOR COLIN HARWOOD (UNIVERSITY OF NEWCASTLE UPON TYNE, UK)
    Strain: AMES
    Synonym: THII

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:183 , LEU A:184 , SER A:185 , SER A:190 , VAL A:207 , HIS A:208 , PHE A:209 , ARG A:265 , MET A:268 , GLY A:287 , GLN A:296 , HOH A:2017 , HOH A:2033BINDING SITE FOR RESIDUE AMP A1392

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C5S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C5S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C5S)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THUMPPS51165 THUMP domain profile.THII_BACAN60-165  1A:60-165
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THUMPPS51165 THUMP domain profile.THII_BACAN60-165  2A:60-165

(-) Exons   (0, 0)

(no "Exon" information available for 2C5S)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:372
 aligned with THII_BACAN | Q81KU0 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:389
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382         
           THII_BACAN     3 YEYILVRYGEMTTKGKNRSKFVSTLKDNVKFKLKKFPNIKIDATHDRMYIQLNGEDHEAVSERLKDVFGIHKFNLAMKVPSELEDIKKGALAAFLQVKGDVKTFKITVHRSYKHFPMRTMELLPEIGGHILENTEDITVDVHNPDVNVRVEIRSGYSYIMCDERMGAGGLPVGVGGKVMVLLSGGIDSPVAAYLTMKRGVSVEAVHFHSPPFTSERAKQKVIDLAQELTKYCKRVTLHLVPFTEVQKTINKEIPSSYSMTVMRRMMMRITERIAEERNALAITTGESLGQVASQTLDSMHTINEVTNYPVIRPLITMDKLEIIKIAEEIGTYDISIRPYEDCCTVFTPASPATKPKREKANRFEAKYDFTPLIDEAVANKETMVLQTVE 391
               SCOP domains d2c5sa2 A:3   -173 Thiamine biosynthesis protein ThiI, N-terminal domain                                                                                                   d2c5sa1 A:174-391 Thiamine biosynthesis protein ThiI, C-terminal domain                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...---hhhhhhhhhhhhhhhhhhh......eeee....eeee....hhhhhhhhhh....eeeeeeeeeee.hhhhhhhhhhhhhhh......eeeeeeee.......hhhhhhhhhhhhhhh.....ee......eeeeeee...eeeeeeeeee...........eeeee....hhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhh...ee......hhhhhhhhhhhh.hhhhhh...--------------..hhhhhhhhhh...hhhhhhhhhhhheeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------THUMP  PDB: A:60-165 UniProt: 60-165                                                                      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c5s A   3 YEYILVRYGEM---GKNRSKFVSTLKDNVKFKLKKFPNIKIDATHDRMYIQLNGEDHEAVSERLKDVFGIHKFNLAMKVPSELEDIKKGALAAFLQVKGDVKTFKITVHRSYKHFPMRTMELLPEIGGHILENTEDITVDVHNPDVNVRVEIRSGYSYIMCDERMGAGGLPVGVGGKVMVLLSGGIDSPVAAYLTMKRGVSVEAVHFHSPPFTSERAKQKVIDLAQELTKYCKRVTLHLVPFTEVQKTINKEIPSSYSMTVMRRMMMRITERIAEERNALAITTGESLGQVASQTLDSMHTINEVTNYPVIRPLITMDKLEIIKIAEEIGTYDISIRPY--------------KPKREKANRFEAKYDFTPLIDEAVANKETMVLQTVE 391
                                    12|   |   22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        |-         -   |   362       372       382         
                                     13  17                                                                                                                                                                                                                                                                                                                                 341            356
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C5S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C5S)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (THII_BACAN | Q81KU0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016783    sulfurtransferase activity    Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
    GO:0004810    tRNA adenylyltransferase activity    Catalysis of the reaction: ATP + tRNA(n) = diphosphate + tRNA(n+1).
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0034227    tRNA thio-modification    The addition a sulfur atom to a nucleotide in a tRNA molecule.
    GO:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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