PDBsum entry 1ze1

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protein metals Protein-protein interface(s) links
Lyase PDB id
Jmol PyMol
Protein chains
308 a.a. *
284 a.a. *
_MG ×4
Waters ×108
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Conformational change of pseudouridine 55 synthase upon its association with RNA substrate
Structure: tRNA pseudouridine synthase b. Chain: a, b, c, d. Synonym: tRNA pseudouridine 55 synthase, psi55 synthase, pseudouridylate synthase, uracil hydrolyase. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: trub. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.90Å     R-factor:   0.235     R-free:   0.281
Authors: K.Phannachet,R.H.Huang
Key ref: K.Phannachet and R.H.Huang (2004). Conformational change of pseudouridine 55 synthase upon its association with RNA substrate. Nucleic Acids Res, 32, 1422-1429. PubMed id: 14990747 DOI: 10.1093/nar/gkh287
16-Apr-05     Release date:   26-Apr-05    
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Protein chains
Pfam   ArchSchema ?
Q9WZW0  (TRUB_THEMA) -  tRNA pseudouridine synthase B
309 a.a.
308 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9WZW0  (TRUB_THEMA) -  tRNA pseudouridine synthase B
309 a.a.
284 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.  - tRNA pseudouridine(55) synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: tRNA uridine55 = tRNA pseudouridine55
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     RNA processing   6 terms 
  Biochemical function     isomerase activity     3 terms  


DOI no: 10.1093/nar/gkh287 Nucleic Acids Res 32:1422-1429 (2004)
PubMed id: 14990747  
Conformational change of pseudouridine 55 synthase upon its association with RNA substrate.
K.Phannachet, R.H.Huang.
Pseudouridine 55 synthase (Psi55S) catalyzes isomerization of uridine (U) to pseudouridine (Psi) at position 55 in transfer RNA. The crystal structures of Thermotoga maritima Psi55S, and its complex with RNA, have been determined at 2.9 and 3.0 A resolutions, respectively. Structural comparisons with other families of pseudouridine synthases (PsiS) indicate that Psi55S may acquire its ability to recognize a stem-loop RNA substrate by two insertions of polypeptides into the PsiS core. The structure of apo-Psi55S reveals that these two insertions interact with each other. However, association with RNA substrate induces substantial conformational change in one of the insertions, resulting in disruption of interaction between insertions and association of both insertions with the RNA substrate. Specific interactions between two insertions, as well as between the insertions and the RNA substrate, account for the molecular basis of the conformational change.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21397180 A.Guelorget, and B.Golinelli-Pimpaneau (2011).
Mechanism-based strategies for trapping and crystallizing complexes of RNA-modifying enzymes.
  Structure, 19, 282-291.  
20106954 M.Hengesbach, F.Voigts-Hoffmann, B.Hofmann, and M.Helm (2010).
Formation of a stalled early intermediate of pseudouridine synthesis monitored by real-time FRET.
  RNA, 16, 610-620.  
19298824 A.Alian, A.DeGiovanni, S.L.Griner, J.S.Finer-Moore, and R.M.Stroud (2009).
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
  J Mol Biol, 388, 785-800.
PDB code: 3dh3
19373903 H.Zhou, Q.Liu, W.Yang, Y.Gao, M.Teng, and L.Niu (2009).
Monomeric tRNA (m(7)G46) methyltransferase from Escherichia coli presents a novel structure at the function-essential insertion.
  Proteins, 76, 512-515.
PDB codes: 3dxx 3dxy 3dxz
19598234 S.W.Fan, R.A.George, N.L.Haworth, L.L.Feng, J.Y.Liu, and M.A.Wouters (2009).
Conformational changes in redox pairs of protein structures.
  Protein Sci, 18, 1745-1765.  
18831030 K.Miyazono, Y.Nishimura, Y.Sawano, T.Makino, and M.Tanokura (2008).
Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3.
  Proteins, 73, 1068-1071.
PDB code: 3d79
18952823 P.Gurha, and R.Gupta (2008).
Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA.
  RNA, 14, 2521-2527.  
17668295 A.Matte, Z.Jia, S.Sunita, J.Sivaraman, and M.Cygler (2007).
Insights into the biology of Escherichia coli through structural proteomics.
  J Struct Funct Genomics, 8, 45-55.  
17320904 H.Pan, J.D.Ho, R.M.Stroud, and J.Finer-Moore (2007).
The crystal structure of E. coli rRNA pseudouridine synthase RluE.
  J Mol Biol, 367, 1459-1470.
PDB codes: 2olw 2oml
17803682 I.Pérez-Arellano, J.Gallego, and J.Cervera (2007).
The PUA domain - a structural and functional overview.
  FEBS J, 274, 4972-4984.  
17574834 K.Ye (2007).
H/ACA guide RNAs, proteins and complexes.
  Curr Opin Struct Biol, 17, 287-292.  
17932071 S.G.Ozanick, J.M.Bujnicki, D.S.Sem, and J.T.Anderson (2007).
Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding.
  Nucleic Acids Res, 35, 6808-6819.  
17188032 C.Hoang, J.Chen, C.A.Vizthum, J.M.Kandel, C.S.Hamilton, E.G.Mueller, and A.R.Ferré-D'Amaré (2006).
Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.
  Mol Cell, 24, 535-545.
PDB code: 2i82
17002302 C.S.Hamilton, T.M.Greco, C.A.Vizthum, J.M.Ginter, M.V.Johnston, and E.G.Mueller (2006).
Mechanistic investigations of the pseudouridine synthase RluA using RNA containing 5-fluorouridine.
  Biochemistry, 45, 12029-12038.  
16600901 I.Zegers, D.Gigot, F.van Vliet, C.Tricot, S.Aymerich, J.M.Bujnicki, J.Kosinski, and L.Droogmans (2006).
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.
  Nucleic Acids Res, 34, 1925-1934.
PDB code: 2fca
16920741 M.Roovers, C.Hale, C.Tricot, M.P.Terns, R.M.Terns, H.Grosjean, and L.Droogmans (2006).
Formation of the conserved pseudouridine at position 55 in archaeal tRNA.
  Nucleic Acids Res, 34, 4293-4301.  
  16511038 A.Matte, G.V.Louie, J.Sivaraman, M.Cygler, and S.K.Burley (2005).
Structure of the pseudouridine synthase RsuA from Haemophilus influenzae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 350-354.
PDB code: 1vio
15987897 C.Hoang, C.S.Hamilton, E.G.Mueller, and A.R.Ferré-D'Amaré (2005).
Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain.
  Protein Sci, 14, 2201-2206.
PDB code: 1zl3
16251366 R.Powers, N.Mirkovic, S.Goldsmith-Fischman, T.B.Acton, Y.Chiang, Y.J.Huang, L.Ma, P.K.Rajan, J.R.Cort, M.A.Kennedy, J.Liu, B.Rost, B.Honig, D.Murray, and G.T.Montelione (2005).
Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes.
  Protein Sci, 14, 2849-2861.
PDB code: 1rzw
16286935 T.Hamma, S.L.Reichow, G.Varani, and A.R.Ferré-D'Amaré (2005).
The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs.
  Nat Struct Mol Biol, 12, 1101-1107.
PDB codes: 2apo 2aqa 2aqc
15208439 C.Hoang, and A.R.Ferre-D'Amare (2004).
Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold.
  RNA, 10, 1026-1033.
PDB code: 1sb7
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 code is shown on the right.