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(-) Description

Title :  STRUCTURE OF E. COLI ISOPENTENYL-TRNA TRANSFERASE IN COMPLEX WITH E. COLI TRNA(PHE)
 
Authors :  E. Seif, B. M. Hallberg
Date :  02 Jan 09  (Deposition) - 20 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Trna, Nucleoside Modification, Isopentenyl-Trna Transferase, Miaa, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Seif, B. M. Hallberg
Rna-Protein Mutually Induced Fit: Structure Of Escherichia Coli Isopentenyl-Trna Transferase In Complex With Trna(Phe)
J. Biol. Chem. V. 284 6600 2009
PubMed-ID: 19158097  |  Reference-DOI: 10.1074/JBC.C800235200

(-) Compounds

Molecule 1 - TRNA DELTA(2)-ISOPENTENYLPYROPHOSPHATE TRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: KRX
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B4171, E. COLI, JW4129, MIAA, TRPX
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K12
 
Molecule 2 - TRNA(PHE)
    Chains: C
    Engineered: YES
    Other Details: TRNA WAS PREPARED BY IN-VITRO TRANSCRIPTION WITH T7
    Synthetic: YES
 
Molecule 3 - TRNA(PHE)
    Chains: D
    Engineered: YES
    Other Details: TRNA WAS PREPARED BY IN-VITRO TRANSCRIPTION WITH T7
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 22)

Asymmetric/Biological Unit (1, 22)
No.NameCountTypeFull Name
1CA22Ligand/IonCALCIUM ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR B:284 , ARG B:287 , A D:31BINDING SITE FOR RESIDUE CA B 317
02AC2SOFTWAREG C:70BINDING SITE FOR RESIDUE CA C 75
03AC3SOFTWAREA C:58 , U C:59BINDING SITE FOR RESIDUE CA C 76
04AC4SOFTWAREU C:16 , C C:17 , G C:19BINDING SITE FOR RESIDUE CA C 77
05AC5SOFTWAREA C:7 , U C:8 , A C:14BINDING SITE FOR RESIDUE CA C 78
06AC6SOFTWAREU C:59 , U C:60BINDING SITE FOR RESIDUE CA C 79
07AC7SOFTWAREU C:12BINDING SITE FOR RESIDUE CA C 80
08AC8SOFTWAREG C:27BINDING SITE FOR RESIDUE CA C 81
09AC9SOFTWAREU C:55BINDING SITE FOR RESIDUE CA C 83
10BC1SOFTWAREG D:22 , U D:45 , G D:46BINDING SITE FOR RESIDUE CA D 1
11BC2SOFTWAREU D:12BINDING SITE FOR RESIDUE CA D 73
12BC3SOFTWAREA D:58 , U D:59BINDING SITE FOR RESIDUE CA D 74
13BC4SOFTWAREU D:16 , C D:17 , G D:19BINDING SITE FOR RESIDUE CA D 75
14BC5SOFTWAREU D:60BINDING SITE FOR RESIDUE CA D 76
15BC6SOFTWAREG D:44BINDING SITE FOR RESIDUE CA D 77
16BC7SOFTWAREA D:26 , G D:27BINDING SITE FOR RESIDUE CA D 78
17BC8SOFTWAREG D:70BINDING SITE FOR RESIDUE CA D 79
18BC9SOFTWAREG D:71 , C D:72BINDING SITE FOR RESIDUE CA D 80
19CC1SOFTWAREA D:7 , U D:8 , A D:14BINDING SITE FOR RESIDUE CA D 81

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly B:190 -Asp B:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FOZ)

(-) 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:305
 aligned with MIAA_ECOLI | P16384 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:305
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306     
           MIAA_ECOLI     7 ASLPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVV 311
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhh.eeeee.................hhhhhhhh.ee...........hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhh........eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3foz A   7 ASLPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVV 311
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306     


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with MIAA_ECOLI | P16384 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:303
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308   
           MIAA_ECOLI     9 LPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVV 311
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhh....eeeee...................hhhhhh.ee...........hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhh.........eeeeeeee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.............hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3foz B   9 LPKAIFLMGPTASGKTALAIELRKILPVELISVDSALIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAAEQGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTELTQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQMLASGFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYLEGEISYDEMVYRGVCATRQLAKRQITWLRGWEGVHWLDSEKPEQARDEVLQVV 311
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308   


Chain C from PDB  Type:RNA  Length:74
                                                                                                          
                 3foz C   1 GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCUGGGCAC  74
                                    10        20        30        40        50        60        70    


Chain D from PDB  Type:RNA  Length:69
                                                                                                     
                 3foz D   4 CGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGGGC  72
                                    13        23        33        43        53        63
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3FOZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FOZ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MIAA_ECOLI | P16384)
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:0034605    cellular response to heat    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    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

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        MIAA_ECOLI | P16384: 2zm5 2zxu

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