PDBsum entry 1rdd

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Hydrolase(endoribonuclease) PDB id
Protein chain
155 a.a. *
Waters ×35
* Residue conservation analysis
PDB id:
Name: Hydrolase(endoribonuclease)
Title: Crystal structure of escherichia coli rnase hi in complex with mg2+ at 2.8 angstroms resolution: proof for a single mg2+ site
Structure: Ribonuclease h. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
2.80Å     R-factor:   0.190    
Authors: K.Katayanagi,K.Morikawa
Key ref: K.Katayanagi et al. (1993). Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site. Proteins, 17, 337-346. PubMed id: 8108376
23-Jun-93     Release date:   31-Oct-93    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0A7Y4  (RNH_ECOLI) -  Ribonuclease HI
155 a.a.
155 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Ribonuclease H.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     nucleic acid phosphodiester bond hydrolysis   4 terms 
  Biochemical function     nucleic acid binding     7 terms  


Proteins 17:337-346 (1993)
PubMed id: 8108376  
Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site.
K.Katayanagi, M.Okumura, K.Morikawa.
To obtain more precise insight into the Mg(2+)-binding site essential for RNase HI catalytic activity, we have determined the crystal structure of E. coli RNase HI in complex with Mg2+. The analyzed cocrystal, which is not isomorphous with the Mg(2+)-free crystal previously refined at 1.48 A resolution, was grown at a high MgSO4 concentration more than 100 mM so that even weakly bound Mg2+ sites could be identified. The structure was solved by the molecular replacement method, using the Mg(2+)-free crystal structure as a search model, and was refined to give a final R-value of 0.190 for intensity data from 10 to 2.8 A, using the XPLOR and PROLSQ programs. The backbone structures are in their entirety very similar to each other between the Mg(2+)-bound and the metal-free crystals, except for minor regions in the enzyme interface with the DNA/RNA hybrid. The active center clearly revealed a single Mg2+ atom located at a position almost identical to that previously found by the soaking method. Although the two metal-ion mechanism had been suggested by another group (Yang, W., Hendrickson, W.A., Crouch, R.J., Satow, Y. Science 249:1398-1405, 1990) and partially supported by the crystallographic study of inactive HIV-1 RT RNase H fragment (Davies, J.F., II, Hostomska, Z., Hostomsky, Z., Jordan, S.R., Matthews, D. Science 252:88-95, 1991), the present result excludes the possibility that RNase HI requires two metal-binding sites for activity. In contrast to the features in the metal-free enzyme, the side chains of Asn-44 and Glu-48 are found to form coordinate bonds with Mg2+ in the metal-bound crystal.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21104192 K.Prymula, T.Jadczyk, and I.Roterman (2011).
Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction.
  J Comput Aided Mol Des, 25, 117-133.  
20672157 B.Elsässer, and G.Fels (2010).
Atomistic details of the associative phosphodiester cleavage in human ribonuclease H.
  Phys Chem Chem Phys, 12, 11081-11088.  
19937113 Z.Hobaika, L.Zargarian, R.G.Maroun, O.Mauffret, T.R.Burke, and S.Fermandjian (2010).
HIV-1 integrase and virus and cell DNAs: complex formation and perturbation by inhibitors of integration.
  Neurochem Res, 35, 888-893.  
20004166 D.M.Himmel, K.A.Maegley, T.A.Pauly, J.D.Bauman, K.Das, C.Dharia, A.D.Clark, K.Ryan, M.J.Hickey, R.A.Love, S.H.Hughes, S.Bergqvist, and E.Arnold (2009).
Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site.
  Structure, 17, 1625-1635.
PDB codes: 3ig1 3k2p
19228195 J.J.Champoux, and S.J.Schultz (2009).
Ribonuclease H: properties, substrate specificity and roles in retroviral reverse transcription.
  FEBS J, 276, 1506-1516.  
19228197 T.Tadokoro, and S.Kanaya (2009).
Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes.
  FEBS J, 276, 1482-1493.  
19625255 W.F.Lima, H.Wu, J.G.Nichols, H.Sun, H.M.Murray, and S.T.Crooke (2009).
Binding and cleavage specificities of human Argonaute2.
  J Biol Chem, 284, 26017-26028.  
19808934 Z.Hobaika, L.Zargarian, Y.Boulard, R.G.Maroun, O.Mauffret, and S.Fermandjian (2009).
Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase {alpha}4 helix.
  Nucleic Acids Res, 37, 7691-7700.  
19032786 D.Zhang, H.Xiong, J.Shan, X.Xia, and V.L.Trudeau (2008).
Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3'-5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch.
  Biol Direct, 3, 48.  
18058906 G.Kieseritzky, and E.W.Knapp (2008).
Optimizing pKa computation in proteins with pH adapted conformations.
  Proteins, 71, 1335-1348.  
18261820 S.J.Schultz, and J.J.Champoux (2008).
RNase H activity: structure, specificity, and function in reverse transcription.
  Virus Res, 134, 86.  
17928262 C.R.Faehnle, and L.Joshua-Tor (2007).
Argonautes confront new small RNAs.
  Curr Opin Chem Biol, 11, 569-577.  
17964265 M.Nowotny, S.A.Gaidamakov, R.Ghirlando, S.M.Cerritelli, R.J.Crouch, and W.Yang (2007).
Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription.
  Mol Cell, 28, 264-276.
PDB codes: 2qk9 2qkb 2qkk
16912289 D.Lim, G.G.Gregorio, C.Bingman, E.Martinez-Hackert, W.A.Hendrickson, and S.P.Goff (2006).
Crystal structure of the moloney murine leukemia virus RNase H domain.
  J Virol, 80, 8379-8389.
PDB code: 2hb5
16403028 H.Kochiwa, M.Itaya, M.Tomita, and A.Kanai (2006).
Stage-specific expression of Caenorhabditis elegans ribonuclease H1 enzymes with different substrate specificities and bivalent cation requirements.
  FEBS J, 273, 420-429.  
17085478 T.L.Diamond, and F.D.Bushman (2006).
Role of metal ions in catalysis by HIV integrase analyzed using a quantitative PCR disintegration assay.
  Nucleic Acids Res, 34, 6116-6125.  
15800637 F.V.Rivas, N.H.Tolia, J.J.Song, J.P.Aragon, J.Liu, G.J.Hannon, and L.Joshua-Tor (2005).
Purified Argonaute2 and an siRNA form recombinant human RISC.
  Nat Struct Mol Biol, 12, 340-349.
PDB codes: 1z25 1z26
16081530 N.Baumberger, and D.C.Baulcombe (2005).
Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs.
  Proc Natl Acad Sci U S A, 102, 11928-11933.  
15496518 A.Lingel, and E.Izaurralde (2004).
RNAi: finding the elusive endonuclease.
  RNA, 10, 1675-1679.  
15502360 H.Chon, R.Nakano, N.Ohtani, M.Haruki, K.Takano, M.Morikawa, and S.Kanaya (2004).
Gene cloning and biochemical characterizations of thermostable ribonuclease HIII from Bacillus stearothermophilus.
  Biosci Biotechnol Biochem, 68, 2138-2147.  
15284453 J.J.Song, S.K.Smith, G.J.Hannon, and L.Joshua-Tor (2004).
Crystal structure of Argonaute and its implications for RISC slicer activity.
  Science, 305, 1434-1437.
PDB code: 1u04
14746510 S.T.Crooke (2004).
Progress in antisense technology.
  Annu Rev Med, 55, 61-95.  
15205459 W.F.Lima, J.G.Nichols, H.Wu, T.P.Prakash, M.T.Migawa, T.K.Wyrzykiewicz, B.Bhat, and S.T.Crooke (2004).
Structural requirements at the catalytic site of the heteroduplex substrate for human RNase H1 catalysis.
  J Biol Chem, 279, 36317-36326.  
14627818 K.Klumpp, J.Q.Hang, S.Rajendran, Y.Yang, A.Derosier, P.Wong Kai In, H.Overton, K.E.Parkes, N.Cammack, and J.A.Martin (2003).
Two-metal ion mechanism of RNA cleavage by HIV RNase H and mechanism-based design of selective HIV RNase H inhibitors.
  Nucleic Acids Res, 31, 6852-6859.  
14506260 W.F.Lima, H.Wu, J.G.Nichols, T.P.Prakash, V.Ravikumar, and S.T.Crooke (2003).
Human RNase H1 uses one tryptophan and two lysines to position the enzyme at the 3'-DNA/5'-RNA terminus of the heteroduplex substrate.
  J Biol Chem, 278, 49860-49867.  
12136094 G.F.Gerard, R.J.Potter, M.D.Smith, K.Rosenthal, G.Dhariwal, J.Lee, and D.K.Chatterjee (2002).
The role of template-primer in protection of reverse transcriptase from thermal inactivation.
  Nucleic Acids Res, 30, 3118-3129.  
12324397 R.E.Georgescu, E.G.Alexov, and M.R.Gunner (2002).
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
  Biophys J, 83, 1731-1748.  
11343799 Y.Tsunaka, M.Haruki, M.Morikawa, and S.Kanaya (2001).
Strong nucleic acid binding to the Escherichia coli RNase HI mutant with two arginine residues at the active site.
  Biochim Biophys Acta, 1547, 135-142.  
  11106164 E.R.Goedken, J.L.Keck, J.M.Berger, and S.Marqusee (2000).
Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI.
  Protein Sci, 9, 1914-1921.
PDB code: 1f21
  10739241 W.Dall'Acqua, and P.Carter (2000).
Substrate-assisted catalysis: molecular basis and biological significance.
  Protein Sci, 9, 1-9.  
11087377 W.R.Davis, J.Tomsho, S.Nikam, E.M.Cook, D.Somand, and J.A.Peliska (2000).
Inhibition of HIV-1 reverse transcriptase-catalyzed DNA strand transfer reactions by 4-chlorophenylhydrazone of mesoxalic acid.
  Biochemistry, 39, 14279-14291.  
10413462 J.Greenwald, V.Le, S.L.Butler, F.D.Bushman, and S.Choe (1999).
The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity.
  Biochemistry, 38, 8892-8898.
PDB codes: 1b92 1b9d 1b9f
  9512096 H.Wu, W.F.Lima, and S.T.Crooke (1998).
Molecular cloning and expression of cDNA for human RNase H.
  Antisense Nucleic Acid Drug Dev, 8, 53-61.  
9852071 J.L.Keck, E.R.Goedken, and S.Marqusee (1998).
Activation/attenuation model for RNase H. A one-metal mechanism with second-metal inhibition.
  J Biol Chem, 273, 34128-34133.  
9813108 K.Ichiyanagi, H.Iwasaki, T.Hishida, and H.Shinagawa (1998).
Mutational analysis on structure-function relationship of a holliday junction specific endonuclease RuvC.
  Genes Cells, 3, 575-586.  
9164453 A.Wlodawer (1997).
Deposition of macromolecular coordinates resulting from crystallographic and NMR studies.
  Nat Struct Biol, 4, 173-174.  
9241229 I.S.Mian (1997).
Comparative sequence analysis of ribonucleases HII, III, II PH and D.
  Nucleic Acids Res, 25, 3187-3195.  
9268340 M.Haruki, E.Noguchi, S.Kanaya, and R.J.Crouch (1997).
Kinetic and stoichiometric analysis for the binding of Escherichia coli ribonuclease HI to RNA-DNA hybrids using surface plasmon resonance.
  J Biol Chem, 272, 22015-22022.  
9161051 M.Thomas, and L.Brady (1997).
HIV integrase: a target for AIDS therapeutics.
  Trends Biotechnol, 15, 167-172.  
  9190796 Y.B.Zhang, S.Ayalew, and S.A.Lacks (1997).
The rnhB gene encoding RNase HII of Streptococcus pneumoniae and evidence of conserved motifs in eucaryotic genes.
  J Bacteriol, 179, 3828-3836.  
8805516 G.Bujacz, M.Jaskólski, J.Alexandratos, A.Wlodawer, G.Merkel, R.A.Katz, and A.M.Skalka (1996).
The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations.
  Structure, 4, 89-96.
PDB codes: 1vsd 1vse 1vsf
8783394 H.Nakamura (1996).
Roles of electrostatic interaction in proteins.
  Q Rev Biophys, 29, 1.  
8702660 M.D.Andrake, and A.M.Skalka (1996).
Retroviral integrase, putting the pieces together.
  J Biol Chem, 271, 19633-19636.  
8576137 S.W.Blain, and S.P.Goff (1996).
Differential effects of Moloney murine leukemia virus reverse transcriptase mutations on RNase H activity in Mg2+ and Mn2+.
  J Biol Chem, 271, 1448-1454.  
7638215 A.Saito, H.Iwasaki, M.Ariyoshi, K.Morikawa, and H.Shinagawa (1995).
Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase.
  Proc Natl Acad Sci U S A, 92, 7470-7474.  
7535929 J.L.Keck, and S.Marqusee (1995).
Substitution of a highly basic helix/loop sequence into the RNase H domain of human immunodeficiency virus reverse transcriptase restores its Mn(2+)-dependent RNase H activity.
  Proc Natl Acad Sci U S A, 92, 2740-2744.  
8535785 J.Ren, R.Esnouf, A.Hopkins, C.Ross, Y.Jones, D.Stammers, and D.Stuart (1995).
The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design.
  Structure, 3, 915-926.
PDB code: 1rev
7735828 W.Yang, and T.A.Steitz (1995).
Recombining the structures of HIV integrase, RuvC and RNase H.
  Structure, 3, 131-134.  
7923356 M.Ariyoshi, D.G.Vassylyev, H.Iwasaki, H.Nakamura, H.Shinagawa, and K.Morikawa (1994).
Atomic structure of the RuvC resolvase: a holliday junction-specific endonuclease from E. coli.
  Cell, 78, 1063-1072.
PDB code: 1hjr
8078761 P.Friedhoff, O.Gimadutdinow, and A.Pingoud (1994).
Identification of catalytically relevant amino acids of the extracellular Serratia marcescens endonuclease by alignment-guided mutagenesis.
  Nucleic Acids Res, 22, 3280-3287.  
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.