PDBsum entry 3fc3

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protein dna_rna ligands metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
189 a.a. *
_NA ×3
_ZN ×4
Waters ×397
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure of the beta-beta-alpha-me type ii restrict endonuclease hpy99i
Structure: Restriction endonuclease hpy99i. Chain: a, b. Engineered: yes. 5'-( Dcp Dtp Dcp Dgp Dap Dcp Dgp Dtp Dap Dgp Da)- chain: c. Engineered: yes. 5'-( Dtp Dap Dcp Dgp Dtp Dcp Dgp Dap Dgp Dtp Dc)- chain: d. Engineered: yes
Source: Helicobacter pylori. Organism_taxid: 85963. Strain: j99. Gene: jhp_0755, synthetic gene codon optimized for escheric expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic DNA. Other_details: synthetic DNA
1.75Å     R-factor:   0.182     R-free:   0.205
Authors: M.Sokolowska,H.Czapinska,M.Bochtler
Key ref: M.Sokolowska et al. (2009). Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA. Nucleic Acids Res, 37, 3799-3810. PubMed id: 19380375
21-Nov-08     Release date:   31-Mar-09    
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Protein chains
Pfam   ArchSchema ?
Q9ZL26  (Q9ZL26_HELPJ) -  Putative
190 a.a.
189 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  


Nucleic Acids Res 37:3799-3810 (2009)
PubMed id: 19380375  
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
M.Sokolowska, H.Czapinska, M.Bochtler.
The beta beta alpha-Me restriction endonuclease (REase) Hpy99I recognizes the CGWCG target sequence and cleaves it with unusual stagger (five nucleotide 5'-recessed ends). Here we present the crystal structure of the specific complex of the dimeric enzyme with DNA. The Hpy99I protomer consists of an antiparallel beta-barrel and two beta 4 alpha 2 repeats. Each repeat coordinates a structural zinc ion with four cysteine thiolates in two CXXC motifs. The beta beta alpha-Me region of the second beta 4 alpha 2 repeat holds the catalytic metal ion (or its sodium surrogate) via Asp148 and Asn165 and activates a water molecule with the general base His149. In the specific complex, Hpy99I forms a ring-like structure around the DNA that contacts DNA bases on the major and minor groove sides via the first and second beta 4 alpha 2 repeats, respectively. Hpy99I interacts with the central base pair of the recognition sequence only on the minor groove side, where A:T resembles T:A and G:C is similar to C:G. The Hpy99I-DNA co-crystal structure provides the first detailed illustration of the beta beta alpha-Me site in REases and complements structural information on the use of this active site motif in other groups of endonucleases such as homing endonucleases (e.g. I-PpoI) and Holliday junction resolvases (e.g. T4 endonuclease VII).

Literature references that cite this PDB file's key reference

  PubMed id Reference
21220111 B.L.Stoddard (2011).
Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.
  Structure, 19, 7.  
21297639 J.H.Chang, S.Xiang, K.Xiang, J.L.Manley, and L.Tong (2011).
Structural and biochemical studies of the 5'→3' exoribonuclease Xrn1.
  Nat Struct Mol Biol, 18, 270-276.
PDB codes: 3pie 3pif
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
20935048 M.Sokolowska, H.Czapinska, and M.Bochtler (2011).
Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
  Nucleic Acids Res, 39, 1554-1564.
PDB codes: 3oqg 3or3
20805246 S.H.Chan, B.L.Stoddard, and S.Y.Xu (2011).
Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.
  Nucleic Acids Res, 39, 1.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20541511 B.W.Shen, D.F.Heiter, S.H.Chan, H.Wang, S.Y.Xu, R.D.Morgan, G.G.Wilson, and B.L.Stoddard (2010).
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
  Structure, 18, 734-743.
PDB codes: 3ldy 3m7k
20071747 F.Khan, Y.Furuta, M.Kawai, K.H.Kaminska, K.Ishikawa, J.M.Bujnicki, and I.Kobayashi (2010).
A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).
  Nucleic Acids Res, 38, 3019-3030.  
20702422 I.A.Murray, S.K.Stickel, and R.J.Roberts (2010).
Sequence-specific cleavage of RNA by Type II restriction enzymes.
  Nucleic Acids Res, 38, 8257-8268.  
19747545 P.Zhang, P.H.Too, J.C.Samuelson, S.H.Chan, T.Vincze, S.Doucette, S.Bäckström, K.D.Potamousis, T.M.Schramm, D.Forrest, D.C.Schwartz, and S.Y.Xu (2010).
Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.
  Protein Expr Purif, 69, 226-234.  
20140205 S.H.Chan, L.Opitz, L.Higgins, D.O'loane, and S.Y.Xu (2010).
Cofactor requirement of HpyAV restriction endonuclease.
  PLoS One, 5, e9071.  
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.