PDBsum entry 1m68

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Structural genomics, unknown function PDB id
Jmol PyMol
Protein chain
234 a.a. *
SO4 ×2
_ZN ×3
Waters ×188
* Residue conservation analysis
PDB id:
Name: Structural genomics, unknown function
Title: Ycdx protein, trinuclear zinc site
Structure: Hypothetical protein ycdx. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Trimer (from PDB file)
2.30Å     R-factor:   0.165     R-free:   0.225
Authors: A.Teplyakov,G.Obmolova,P.P.Khil,R.D.Camerini-Otero,G.L.Gilli
Key ref:
A.Teplyakov et al. (2003). Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site. Proteins, 51, 315-318. PubMed id: 12661000 DOI: 10.1002/prot.10352
14-Jul-02     Release date:   22-Apr-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P75914  (YCDX_ECOLI) -  Probable phosphatase YcdX
245 a.a.
234 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     DNA biosynthetic process   3 terms 
  Biochemical function     catalytic activity     8 terms  


DOI no: 10.1002/prot.10352 Proteins 51:315-318 (2003)
PubMed id: 12661000  
Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site.
A.Teplyakov, G.Obmolova, P.P.Khil, A.J.Howard, R.D.Camerini-Otero, G.L.Gilliland.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. Ribbon presentation of the polypeptide fold of YcdX. A disordered loop 162-170 is shown in white. The blue spheres indicate zinc ions in the active site.
Figure 2.
Figure 2. Stereoview of the trinuclear zinc cluster in YcdX. Zn1 is the high-affinity site occupied by zinc in the native structure. Smaller spheres represent water molecules. Potential hydrogen bonds are shown as dashed lines.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2003, 51, 315-318) copyright 2003.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20974932 B.Baños, L.Villar, M.Salas, and Vega (2010).
Intrinsic apurinic/apyrimidinic (AP) endonuclease activity enables Bacillus subtilis DNA polymerase X to recognize, incise, and further repair abasic sites.
  Proc Natl Acad Sci U S A, 107, 19219-19224.  
19548090 D.Bandyopadhyay, J.Huan, J.Prins, J.Snoeyink, W.Wang, and A.Tropsha (2009).
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications.
  J Comput Aided Mol Des, 23, 785-797.  
19221587 K.Chen, and L.Kurgan (2009).
Investigation of atomic level patterns in protein--small ligand interactions.
  PLoS ONE, 4, e4473.  
19508719 O.V.Kalinina, M.S.Gelfand, and R.B.Russell (2009).
Combining specificity determining and conserved residues improves functional site prediction.
  BMC Bioinformatics, 10, 174.  
19482467 R.I.Sadreyev, B.H.Kim, and N.V.Grishin (2009).
Discrete-continuous duality of protein structure space.
  Curr Opin Struct Biol, 19, 321-328.  
19211662 S.Nakane, N.Nakagawa, S.Kuramitsu, and R.Masui (2009).
Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity.
  Nucleic Acids Res, 37, 2037-2052.  
18776221 B.Baños, J.M.Lázaro, L.Villar, M.Salas, and Vega (2008).
Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase.
  Nucleic Acids Res, 36, 5736-5749.  
17346342 A.Schlicker, J.Rahnenführer, M.Albrecht, T.Lengauer, and F.S.Domingues (2007).
GOTax: investigating biological processes and biochemical activities along the taxonomic tree.
  Genome Biol, 8, R33.  
16510973 A.Dickmanns, M.Ballschmiter, W.Liebl, and R.Ficner (2006).
Structure of the novel alpha-amylase AmyC from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 62, 262-270.
PDB code: 2b5d
16517598 A.Wieczorek, and C.S.McHenry (2006).
The NH2-terminal php domain of the alpha subunit of the Escherichia coli replicase binds the epsilon proofreading subunit.
  J Biol Chem, 281, 12561-12567.  
16731985 D.Bandyopadhyay, J.Huan, J.Liu, J.Prins, J.Snoeyink, W.Wang, and A.Tropsha (2006).
Structure-based function inference using protein family-specific fingerprints.
  Protein Sci, 15, 1537-1543.  
16565070 K.L.Damm, and H.A.Carlson (2006).
Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures.
  Biophys J, 90, 4558-4573.  
16959568 M.H.Lamers, R.E.Georgescu, S.G.Lee, M.O'Donnell, and J.Kuriyan (2006).
Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III.
  Cell, 126, 881-892.
PDB codes: 2hnh 2hqa
16604084 N.M.Stano, J.Chen, and C.S.McHenry (2006).
A coproofreading Zn(2+)-dependent exonuclease within a bacterial replicase.
  Nat Struct Mol Biol, 13, 458-459.  
16959569 S.Bailey, R.A.Wing, and T.A.Steitz (2006).
The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.
  Cell, 126, 893-904.
PDB codes: 2hpi 2hpm
15613537 M.Dlakić (2005).
3D models of yeast RNase P/MRP proteins Rpp1p and Pop3p.
  RNA, 11, 123-127.  
15036155 A.F.Yakunin, A.A.Yee, A.Savchenko, A.M.Edwards, and C.H.Arrowsmith (2004).
Structural proteomics: a tool for genome annotation.
  Curr Opin Chem Biol, 8, 42-48.  
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.