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protein metals links
Hydrolase PDB id
1dbu
Jmol
Contents
Protein chain
152 a.a. *
Metals
_HG
Waters ×171
* Residue conservation analysis
PDB id:
1dbu
Name: Hydrolase
Title: Crystal structure of cysteinyl-tRNA(pro) deacylase protein from h. Influenzae (hi1434)
Structure: Cysteinyl-tRNA(pro) deacylase. Chain: a. Synonym: hi1434. Engineered: yes
Source: Haemophilus influenzae. Organism_taxid: 727. Gene: ybak. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: impact i system from new england biolabs
Resolution:
1.80Å     R-factor:   0.193     R-free:   0.262
Authors: H.Zhang,K.Huang,Z.Li,O.Herzberg,Structure 2 Function Project (S2f)
Key ref:
H.Zhang et al. (2000). Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications. Proteins, 40, 86-97. PubMed id: 10813833 DOI: 10.1002/(SICI)1097-0134(20000701)40:1<86::AID-PROT100>3.0.CO;2-Y
Date:
03-Nov-99     Release date:   14-Jun-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P45202  (YBAK_HAEIN) -  Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase ybaK
Seq:
Struc: 		158 a.a.
152 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     Ala-tRNA(Pro) hydrolase activity     1 term  

 

 
DOI no: 10.1002/(SICI)1097-0134(20000701)40:1<86::AID-PROT100>3.0.CO;2-Y Proteins 40:86-97 (2000)
PubMed id: 10813833  
 
 
Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.
H.Zhang, K.Huang, Z.Li, L.Banerjei, K.E.Fisher, N.V.Grishin, E.Eisenstein, O.Herzberg.
 
  ABSTRACT  
 
Structural genomics of proteins of unknown function most straightforwardly assists with assignment of biochemical activity when the new structure resembles that of proteins whose functions are known. When a new fold is revealed, the universe of known folds is enriched, and once the function is determined by other means, novel structure-function relationships are established. The previously unannotated protein HI1434 from H. influenzae provides a hybrid example of these two paradigms. It is a member of a microbial protein family, labeled in SwissProt as YbaK and ebsC. The crystal structure at 1.8 A resolution reported here reveals a fold that is only remotely related to the C-lectin fold, in particular to endostatin, and thus is not sufficiently similar to imply that YbaK proteins are saccharide binding proteins. However, a crevice that may accommodate a small ligand is evident. The putative binding site contains only one invariant residue, Lys46, which carries a functional group that could play a role in catalysis, indicating that YbaK is probably not an enzyme. Detailed sequence analysis, including a number of newly sequenced microbial organisms, highlights sequence homology to an insertion domain in prolyl-tRNA synthetases (proRS) from prokaryote, a domain whose function is unknown. A HI1434-based model of the insertion domain shows that it should also contain the putative binding site. Being part of a tRNA synthetases, the insertion domain is likely to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA. By analogy, YbaK may also play a role in nucleotide or oligonucleotide binding, the nature of which is yet to be determined.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structure of YbaK. A) Ribbon diagram of YbaK prepared using Molscript,[55] gl-render (Lothar Esser, unpublished program), and POV-ray (http://povray.org/), rainbow colored from N- to C terminus. strands are labeled from a-h, helices A-F. B) Topological diagram of the arrangement of the secondary structure elements of YbaK. Triangles represent strands and circles represent helices. The N and C termini are marked. C) Stereo view of the trace of the C atom positions, shown in the same orientation as in A. Every 20th residue is numbered. 		Figure 3.
Figure 3. Molecular surface of YbaK. The surface is colored according to electrostatic potential using GRASP.[56] Blue represents regions of positive potential and red regions of negative potential. A) The positively charged patch. B) Rotation of 90° about the page vertical axis from the view shown in A, displaying the putative ligand binding site.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2000, 40, 86-97) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18241793 K.E.Splan, K.Musier-Forsyth, M.T.Boniecki, and S.A.Martinis (2008).
In vitro assays for the determination of aminoacyl-tRNA synthetase editing activity.
  Methods, 44, 119-128.  
18180290 K.E.Splan, M.E.Ignatov, and K.Musier-Forsyth (2008).
Transfer RNA modulates the editing mechanism used by class II prolyl-tRNA synthetase.
  J Biol Chem, 283, 7128-7134.  
17283340 J.SternJohn, S.Hati, P.G.Siliciano, and K.Musier-Forsyth (2007).
Restoring species-specific posttransfer editing activity to a synthetase with a defunct editing domain.
  Proc Natl Acad Sci U S A, 104, 2127-2132.  
16870930 B.Song, J.H.Choi, G.Chen, J.Szymanski, G.Q.Zhang, A.K.Tung, J.Kang, S.Kim, and J.Yang (2006).
ARCS: an aggregated related column scoring scheme for aligned sequences.
  Bioinformatics, 22, 2326-2332.  
17027500 T.Crepin, A.Yaremchuk, M.Tukalo, and S.Cusack (2006).
Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain.
  Structure, 14, 1511-1525.
PDB codes: 2i4l 2i4m 2i4n 2i4o 2j3l 2j3m
16187365 A.Kryshtafovych, C.Venclovas, K.Fidelis, and J.Moult (2005).
Progress over the first decade of CASP experiments.
  Proteins, 61, 225-236.  
15886196 B.Ruan, and D.Söll (2005).
The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase.
  J Biol Chem, 280, 25887-25891.  
  16508081 K.Murayama, M.Kato-Murayama, K.Katsura, T.Uchikubo-Kamo, M.Yamaguchi-Hirafuji, M.Kawazoe, R.Akasaka, K.Hanawa-Suetsugu, C.Hori-Takemoto, T.Terada, M.Shirouzu, and S.Yokoyama (2005).
Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 26-29.
PDB code: 1wdv
15840833 P.K.Shah, P.Aloy, P.Bork, and R.B.Russell (2005).
Structural similarity to bridge sequence space: finding new families on the bridges.
  Protein Sci, 14, 1305-1314.  
16087664 S.An, and K.Musier-Forsyth (2005).
Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase.YbaK.tRNA ternary complex.
  J Biol Chem, 280, 34465-34472.  
15231779 N.C.Caiazza, and G.A.O'Toole (2004).
SadB is required for the transition from reversible to irreversible attachment during biofilm formation by Pseudomonas aeruginosa PA14.
  J Bacteriol, 186, 4476-4485.  
15322138 S.An, and K.Musier-Forsyth (2004).
Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein.
  J Biol Chem, 279, 42359-42362.  
15094797 Y.Zheng, R.J.Roberts, and S.Kasif (2004).
Segmentally variable genes: a new perspective on adaptation.
  PLoS Biol, 2, E81.  
12837772 A.Matte, J.Sivaraman, I.Ekiel, K.Gehring, Z.Jia, and M.Cygler (2003).
Contribution of structural genomics to understanding the biology of Escherichia coli.
  J Bacteriol, 185, 3994-4002.  
14530268 F.C.Wong, P.J.Beuning, C.Silvers, and K.Musier-Forsyth (2003).
An isolated class II aminoacyl-tRNA synthetase insertion domain is functional in amino acid editing.
  J Biol Chem, 278, 52857-52864.  
14663147 I.Ahel, D.Korencic, M.Ibba, and D.Söll (2003).
Trans-editing of mischarged tRNAs.
  Proc Natl Acad Sci U S A, 100, 15422-15427.  
12832765 T.Wada, M.Shirouzu, T.Terada, Y.Ishizuka, T.Matsuda, T.Kigawa, S.Kuramitsu, S.Y.Park, J.R.Tame, and S.Yokoyama (2003).
Structure of a conserved CoA-binding protein synthesized by a cell-free system.
  Acta Crystallogr D Biol Crystallogr, 59, 1213-1218.
PDB codes: 1iuk 1iul
12091873 M.A.Bianchet, E.W.Odom, G.R.Vasta, and L.M.Amzel (2002).
A novel fucose recognition fold involved in innate immunity.
  Nat Struct Biol, 9, 628-634.
PDB code: 1k12
12077430 M.D.Purdy, P.Ge, J.Chen, P.R.Selvin, and M.C.Wiener (2002).
Thiol-reactive lanthanide chelates for phasing protein X-ray diffraction data.
  Acta Crystallogr D Biol Crystallogr, 58, 1111-1117.  
  12537566 M.P.Joachimiak, and F.E.Cohen (2002).
JEvTrace: refinement and variations of the evolutionary trace in JAVA.
  Genome Biol, 3, RESEARCH0077.  
  11470603 P.R.Mittl, and M.G.Grütter (2001).
Structural genomics: opportunities and challenges.
  Curr Opin Chem Biol, 5, 402-408.  
11406387 S.A.Teichmann, A.G.Murzin, and C.Chothia (2001).
Determination of protein function, evolution and interactions by structural genomics.
  Curr Opin Struct Biol, 11, 354-363.  
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.