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PDBsum entry 2vqf
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
2vqf

 

 

 

 

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Contents
Protein chains
235 a.a. *
207 a.a. *
208 a.a. *
151 a.a. *
101 a.a. *
155 a.a. *
138 a.a. *
127 a.a. *
99 a.a. *
119 a.a. *
125 a.a. *
125 a.a. *
60 a.a. *
88 a.a. *
84 a.a. *
104 a.a. *
73 a.a. *
81 a.a. *
99 a.a. *
25 a.a. *
DNA/RNA
Ligands
PAR
Metals
_MG ×214
__K ×73
_ZN ×2
* Residue conservation analysis
PDB id:
2vqf
Name: Ribosome
Title: Modified uridines with c5-methylene substituents at the first position of the tRNA anticodon stabilize u-g wobble pairing during decoding
Structure: 16s rrna. Chain: a. Other_details: chain a (16s RNA) has e.Coli numbering, based on a structural alignment with the corresponding e.Coli structure in 2avy. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Strain: hb8
Resolution:
2.90Å     R-factor:   0.223     R-free:   0.258
Authors: S.Kurata,A.Weixlbaumer,T.Ohtsuki,T.Shimazaki,T.Wada,Y.Kirino,K.Takai, K.Watanabe,V.Ramakrishnan,T.Suzuki
Key ref:
S.Kurata et al. (2008). Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding. J Biol Chem, 283, 18801-18811. PubMed id: 18456657 DOI: 10.1074/jbc.M800233200
Date:
14-Mar-08     Release date:   29-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		256 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		239 a.a.
207 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		162 a.a.
151 a.a.
Protein chain
Q5SLP8  (RS6_THET8) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
P0DOY9  (RS8_THET8) -  Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		105 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		132 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		126 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P0DOY6  (RS14Z_THET8) -  Small ribosomal subunit protein uS14 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P0DOY7  (RS17_THET8) -  Small ribosomal subunit protein uS17 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		105 a.a.
104 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		93 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		106 a.a.
99 a.a.*
Protein chain
Q5SIH3  (RSHX_THET8) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		27 a.a.
25 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains
  U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1513 bases
  U-U-G-A 4 bases
  U-TM2-A-A-A-A-C 7 bases

 Enzyme reactions 
   Enzyme class: Chains B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1074/jbc.M800233200 J Biol Chem 283:18801-18811 (2008)
PubMed id: 18456657  
 
 
Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding.
S.Kurata, A.Weixlbaumer, T.Ohtsuki, T.Shimazaki, T.Wada, Y.Kirino, K.Takai, K.Watanabe, V.Ramakrishnan, T.Suzuki.
 
  ABSTRACT  
 
Post-transcriptional modifications at the first (wobble) position of the tRNA anticodon participate in precise decoding of the genetic code. To decode codons that end in a purine (R) (i.e. NNR), tRNAs frequently utilize 5-methyluridine derivatives (xm(5)U) at the wobble position. However, the functional properties of the C5-substituents of xm(5)U in codon recognition remain elusive. We previously found that mitochondrial tRNAs(Leu(UUR)) with pathogenic point mutations isolated from MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) patients lacked the 5-taurinomethyluridine (taum(5)U) modification and caused a decoding defect. Here, we constructed Escherichia coli tRNAs(Leu(UUR)) with or without xm(5)U modifications at the wobble position and measured their decoding activities in an in vitro translation as well as by A-site tRNA binding. In addition, the decoding properties of tRNA(Arg) lacking mnm(5)U modification in a knock-out strain of the modifying enzyme (DeltamnmE) were examined by pulse labeling using reporter constructs with consecutive AGR codons. Our results demonstrate that the xm(5)U modification plays a critical role in decoding NNG codons by stabilizing U.G pairing at the wobble position. Crystal structures of an anticodon stem-loop containing taum(5)U interacting with a UUA or UUG codon at the ribosomal A-site revealed that the taum(5)U.G base pair does not have classical U.G wobble geometry. These structures provide help to explain how the taum(5)U modification enables efficient decoding of UUG codons.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Construction of E. coli tRNA^Leu(UUR) bearing wobble modifications. A, chemical structures of the modified uridines introduced into the wobble position of E. coli tRNA^Leu(UUR): cmnm^5U and m^5U. B, cloverleaf structure of E. coli tRNA^Leu(UUR). U^*, the modified uridine. C, schematic depiction of the molecular surgery procedure used to construct E. coli tRNA^Leu(UUR) bearing the wobble modifications. The details are described under "Experimental Procedures." BAP, bacterial alkaline phosphatase; PNK, polynucleotide kinase. 		Figure 5.
FIGURE 5. Crystal structures of an interacting with either UUA or UUG in the ribosomal A-site. A, unbiased difference Fourier electron density maps for ASL and mRNA (green mesh) are shown in stereo for the complex with the UUA codon. The 5' part of the ASL up to and including parts of U33 is not visible. B, the same as A but for the complex having a UUG codon in the A-site. C, the m^5U-A base pair along with unbiased difference Fourier electron density maps (green mesh). The base pair refined into a position with slightly distorted WC geometry. Weak density for the sulfonic acid group was visible at this level. D, the m^5U·G base pair with unbiased difference Fourier electron density maps (green mesh). Although the density is not very strong, it can be excluded that the base pair adopts G·U wobble geometry (compare modeled G·U base pair in transparent gray with electron density maps). E, comparison of stacking interaction between a modeled G·U wobble base pair and the m^5U·G base pair. The modified uridine has a more favorable stacking interaction with A35 than an unmodified base would have.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 18801-18811) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21134891 P.Benkert, M.Biasini, and T.Schwede (2011).
Toward the estimation of the absolute quality of individual protein structure models.
  Bioinformatics, 27, 343-350.  
20689681 N.B.Ulyanov, and T.L.James (2010).
RNA structural motifs that entail hydrogen bonds involving sugar-phosphate backbone atoms of RNA.
  New J Chem, 34, 910-917.  
19151083 C.Takemoto, L.L.Spremulli, L.A.Benkowski, T.Ueda, T.Yokogawa, and K.Watanabe (2009).
Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system.
  Nucleic Acids Res, 37, 1616-1627.  
19285505 H.Demirci, R.Belardinelli, E.Seri, S.T.Gregory, C.Gualerzi, A.E.Dahlberg, and G.Jogl (2009).
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.
  J Mol Biol, 388, 271-282.
PDB codes: 3fut 3fuu 3fuv 3fuw 3fux
19767610 I.Moukadiri, S.Prado, J.Piera, A.Velázquez-Campoy, G.R.Björk, and M.E.Armengod (2009).
Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions.
  Nucleic Acids Res, 37, 7177-7193.  
19417106 M.Frechin, B.Senger, M.Brayé, D.Kern, R.P.Martin, and H.D.Becker (2009).
Yeast mitochondrial Gln-tRNA(Gln) is generated by a GatFAB-mediated transamidation pathway involving Arc1p-controlled subcellular sorting of cytosolic GluRS.
  Genes Dev, 23, 1119-1130.  
19446527 T.Osawa, K.Ito, H.Inanaga, O.Nureki, K.Tomita, and T.Numata (2009).
Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon.
  Structure, 17, 713-724.
PDB codes: 2zxh 2zxi
18927116 H.Lusic, E.M.Gustilo, F.A.Vendeix, R.Kaiser, M.O.Delaney, W.D.Graham, V.A.Moye, W.A.Cantara, P.F.Agris, and A.Deiters (2008).
Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNAMet.
  Nucleic Acids Res, 36, 6548-6557.  
18638409 X.Xia (2008).
The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses.
  BMC Evol Biol, 8, 211.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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