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(-) Description

Title :  CRYSTAL STRUCTURE OF A. AEOLICUS TRMH/SPOU TRNA MODIFYING ENZYME
 
Authors :  E. Pleshe, J. Truesdell, R. T. Batey
Date :  30 Apr 05  (Deposition) - 09 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Methylase, Rna Modifying Enzyme, Topological Knot, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Pleshe, J. Truesdell, R. T. Batey
Structure Of A Class Ii Trmh Trna-Modifying Enzyme From Aquifex Aeolicus.
Acta Crystallogr. , Sect. F V. 61 722 2005
PubMed-ID: 16511140  |  Reference-DOI: 10.1107/S1744309105022980

(-) Compounds

Molecule 1 - TRNA (GUANOSINE-2'-O-)-METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.34
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRXB
    Expression System Strain: ROSETTA(DE3)/PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRMH, SPOU
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: TRNA [GM18] METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:35 , HIS A:37 , ASN A:38 , ARG A:44 , ILE A:70 , ASN A:156 , HOH A:547 , HOH A:561BINDING SITE FOR RESIDUE SO4 A 212
2AC2SOFTWARETHR A:103 , VAL A:125 , GLY A:126 , SER A:154 , LEU A:155 , VAL A:157 , ALA A:160 , GOL A:530BINDING SITE FOR RESIDUE GOL A 529
3AC3SOFTWAREASN A:127 , GLU A:128 , LEU A:129 , GLY A:131 , GOL A:529 , HOH A:569 , HOH A:600 , HOH A:607 , HOH A:650BINDING SITE FOR RESIDUE GOL A 530
4AC4SOFTWAREVAL A:33 , LYS A:34 , GLU A:36 , PHE A:39 , HIS A:58 , ALA A:64 , LYS A:65 , HOH A:627 , HOH A:628BINDING SITE FOR RESIDUE GOL A 531

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZJR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZJR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZJR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZJR)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZJR)

(-) 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:197
 aligned with TRMH_AQUAE | O67577 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:197
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       
           TRMH_AQUAE     6 LVLEKRLKRLREVLEKRQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAEGKKAKINEGITQGSHKWVFIEKVDNPVQKLLEFKNRGFQIVATWLSKESVNFREVDYTKPTVLVVGNELQGVSPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQRQREEKGMYSRPSLSEEEIQKILKKWAYEDVIK 202
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zjrA00 A:6-202  [code=3.40.1280.10, no name defined]                                                                                                                                                 CATH domains
               Pfam domains -------------------SpoU_methylase-1zjrA01 A:25-166                                                                                                               ---SpoU_methylas_C-1zjrA02 A:170-202 Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhheeeeeee.........hhhhhhhhhhh.eeee..hhhhhhhhhhhh..eeeee......ee.hhh.....eeeeee......hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zjr A   6 LVLEKRLKRLREVLEKRQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAEGKKAKINEGITQGSHKWVFIEKVDNPVQKLLEFKNRGFQIVATWLSKESVNFREVDYTKPTVLVVGNELQGVSPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQRQREEKGMYSRPSLSEEEIQKILKKWAYEDVIK 202
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1ZJR)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: SPOUT (28)
(-)
Clan: no clan defined [family: SpoU_methylas_C] (1)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRMH_AQUAE | O67577)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008173    RNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0009020    tRNA (guanosine-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 2'-O-methylguanosine.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0002938    tRNA guanine ribose methylation    The process whereby a guanosine residue in a tRNA is methylated on the 2'-hydroxyl group of the ribose moiety.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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