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(-) Description

Title :  STRUCTURE OF TRNA DIMETHYLALLYLTRANSFERASE: RNA MODIFICATION THROUGH A CHANNEL
 
Authors :  R. H. Huang, W. Xie, C. Zhou
Date :  07 Apr 08  (Deposition) - 29 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Atp-Binding, Nucleotide-Binding, Nucleotidyltransferase, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Xie, C. Zhou, R. H. Huang
Structure Of Trna Dimethylallyltransferase: Rna Modification Through A Channel
J. Mol. Biol. V. 367 872 2007
PubMed-ID: 17292915  |  Reference-DOI: 10.1016/J.JMB.2007.01.048
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA DELTA(2)-ISOPENTENYLPYROPHOSPHATE TRANSFERASE
    Chains: A
    EC Number: 2.5.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PLM-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MIAA
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3CRM)

(-) Sites  (0, 0)

(no "Site" information available for 3CRM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CRM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CRM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CRM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CRM)

(-) Exons   (0, 0)

(no "Exon" information available for 3CRM)

(-) Sequences/Alignments

Asymmetric/Biological 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:236
 aligned with MIAA_PSEAE | Q9HUL9 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:321
                                    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 
           MIAA_PSEAE     3 SLPPAIFLMGPTAAGKTDLAMALADALPCELISVDSALIYRGMDIGTAKPSRELLARYPHRLIDIRDPAESYSAAEFRADALAAMAKATARGRIPLLVGGTMLYYKALLEGLADMPGADPEVRAAIEAEAQAEGWEALHRQLAEVDPESAARIHPNDPQRLMRALEVYRLGGVSMSDLRRRQSAEKADFDASGRNQLPYTVAQLAIAPEQRQVLHARIAQRFRQMLEQGFIAEVEALHARSDLHAGLPSIRAVGYRQVWDYLDGKLSYAEMTERGIIATRQLAKRQFTWLRSWSHLHWMDSLAGDNLPRALKYLKTVSILA 323
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3crmA01 A:3-212,A:297-323 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                    3crmA02 A:213-296                                                                   3crmA01 A:3-212,A:297-323   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhh.eeeeee................hhhhhhhh.ee...........hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh.-------------------------------------------------------------------------------------...eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3crm A   3 SLPPAIFLMGPTAAGKTDLAMALADALPCELISVDSALIYRGMDIGTAKPSRELLARYPHRLIDIRDPAESYSAAEFRADALAAMAKATARGRIPLLVGGTMLYYKALLEG-------------------------------------------------------------------------------------LPYTVAQLAIAPEQRQVLHARIAQRFRQMLEQGFIAEVEALHARSDLHAGLPSIRAVGYRQVWDYLDGKLSYAEMTERGIIATRQLAKRQFTWLRSWSHLHWMDSLAGDNLPRALRYLKTVSILA 323
                                    12        22        32        42        52        62        72        82        92       102       112|        -         -         -         -         -         -         -         -      |202       212       222       232       242       252       262       272       282       292       302       312       322 
                                                                                                                                        113                                                                                   199
   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  (0, 0)

(no "SCOP Domain" information available for 3CRM)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CRM)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MIAA_PSEAE | Q9HUL9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0052381    tRNA dimethylallyltransferase activity    Catalysis of the reaction: dimethylallyl diphosphate + tRNA = diphosphate + tRNA containing 6-dimethylallyladenosine.
    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:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MIAA_PSEAE | Q9HUL9: 3crq 3crr

(-) Related Entries Specified in the PDB File

3crq STRUCTURE OF TRNA DIMETHYLALLYLTRANSFERASE: RNA MODIFICATION THROUGH A CHANNEL
3crr STRUCTURE OF TRNA DIMETHYLALLYLTRANSFERASE: RNA MODIFICATION THROUGH A CHANNEL