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PDBsum entry 1qhg

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protein ligands metals links
Hydrolase PDB id
1qhg
Jmol
Contents
Protein chain
622 a.a. *
Ligands
ATP
Metals
_MG
Waters ×125
* Residue conservation analysis
PDB id:
1qhg
Name: Hydrolase
Title: Structure of DNA helicase mutant with adpnp
Structure: Atp-dependent helicase pcra. Chain: a. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Strain: nca1503. Gene: pcra. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.50Å     R-factor:   0.220     R-free:   0.269
Authors: P.Soultanas,M.S.Dillingham,S.S.Velankar,D.B.Wigley
Key ref:
P.Soultanas et al. (1999). DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase. J Mol Biol, 290, 137-148. PubMed id: 10388562 DOI: 10.1006/jmbi.1999.2873
Date:
14-May-99     Release date:   13-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56255  (PCRA_GEOSE) -  ATP-dependent DNA helicase PcrA
Seq:
Struc:
 
Seq:
Struc:
724 a.a.
622 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+ H(2)O
= ADP
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     DNA unwinding involved in replication   1 term 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.2873 J Mol Biol 290:137-148 (1999)
PubMed id: 10388562  
 
 
DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase.
P.Soultanas, M.S.Dillingham, S.S.Velankar, D.B.Wigley.
 
  ABSTRACT  
 
Based upon the crystal structures of PcrA helicase, we have made and characterised mutations in a number of conserved helicase signature motifs around the ATPase active site. We have also determined structures of complexes of wild-type PcrA with ADPNP and of a mutant PcrA complexed with ADPNP and Mn2+. The kinetic and structural data define roles for a number of different residues in and around the ATP binding site. More importantly, our results also show that there are two functionally distinct conformations of ATP in the active site. In one conformation, ATP is hydrolysed poorly whereas in the other (activated) conformation, ATP is hydrolysed much more rapidly. We propose a mechanism to explain how the stimulation of ATPase activity afforded by binding of single-stranded DNA stabilises the activated conformation favouring Mg2+binding and a consequent repositioning of the gamma-phosphate group which promotes ATP hydrolysis. A part of the associated conformational change in the protein forces the side-chain of K37 to vacate the Mg2+binding site, allowing the cation to bind and interact with ATP.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. A stereo Figure showing the amino acid residues that contribute to the ATPase active site in the crystal structure of the substrate complex (Velankar et al., 1999).
Figure 5.
Figure 5. (a) Electron density in the active site region of the soaked complex. (b) Electron density in the active site region of the K37A soaked complex. (c) A stereo Figure showing a superposition of the active sites of the soaked complex (blue), and the K37A soaked complex (red).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 290, 137-148) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21071401 J.T.Yeeles, E.J.Gwynn, M.R.Webb, and M.S.Dillingham (2011).
The AddAB helicase-nuclease catalyses rapid and processive DNA unwinding using a single Superfamily 1A motor domain.
  Nucleic Acids Res, 39, 2271-2285.  
20089461 A.V.Mazin, O.M.Mazina, D.V.Bugreev, and M.J.Rossi (2010).
Rad54, the motor of homologous recombination.
  DNA Repair (Amst), 9, 286-302.  
20305786 B.Lokesh, P.R.Rashmi, B.S.Amruta, D.Srisathiyanarayanan, M.R.Murthy, and H.S.Savithri (2010).
NSs encoded by groundnut bud necrosis virus is a bifunctional enzyme.
  PLoS One, 5, e9757.  
19317511 K.M.Sinha, M.S.Glickman, and S.Shuman (2009).
Mutational analysis of Mycobacterium UvrD1 identifies functional groups required for ATP hydrolysis, DNA unwinding, and chemomechanical coupling.
  Biochemistry, 48, 4019-4030.  
19748362 M.Honda, J.Park, R.A.Pugh, T.Ha, and M.Spies (2009).
Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase.
  Mol Cell, 35, 694-703.  
18057007 D.E.Kainov, E.J.Mancini, J.Telenius, J.Lísal, J.M.Grimes, D.H.Bamford, D.I.Stuart, and R.Tuma (2008).
Structural basis of mechanochemical coupling in a hexameric molecular motor.
  J Biol Chem, 283, 3607-3617.
PDB codes: 2vhc 2vhj 2vhq 2vht 2vhu
19052323 M.S.Dillingham, and S.C.Kowalczykowski (2008).
RecBCD enzyme and the repair of double-stranded DNA breaks.
  Microbiol Mol Biol Rev, 72, 642.  
18687036 V.B.Rao, and M.Feiss (2008).
The bacteriophage DNA packaging motor.
  Annu Rev Genet, 42, 647-681.  
18400864 W.B.Greenleaf, J.Shen, D.Gai, and X.S.Chen (2008).
Systematic study of the functions for the residues around the nucleotide pocket in simian virus 40 AAA+ hexameric helicase.
  J Virol, 82, 6017-6023.  
17084859 D.N.Frick, S.Banik, and R.S.Rypma (2007).
Role of divalent metal cations in ATP hydrolysis catalyzed by the hepatitis C virus NS3 helicase: magnesium provides a bridge for ATP to fuel unwinding.
  J Mol Biol, 365, 1017-1032.  
17158674 E.Curti, S.J.Smerdon, and E.O.Davis (2007).
Characterization of the helicase activity and substrate specificity of Mycobacterium tuberculosis UvrD.
  J Bacteriol, 189, 1542-1555.  
17766252 H.Ren, S.X.Dou, P.Rigolet, Y.Yang, P.Y.Wang, M.Amor-Gueret, and X.G.Xi (2007).
The arginine finger of the Bloom syndrome protein: its structural organization and its role in energy coupling.
  Nucleic Acids Res, 35, 6029-6041.  
17506634 M.R.Singleton, M.S.Dillingham, and D.B.Wigley (2007).
Structure and mechanism of helicases and nucleic acid translocases.
  Annu Rev Biochem, 76, 23-50.  
17386269 S.Sun, K.Kondabagil, P.M.Gentz, M.G.Rossmann, and V.B.Rao (2007).
The structure of the ATPase that powers DNA packaging into bacteriophage T4 procapsids.
  Mol Cell, 25, 943-949.
PDB codes: 2o0h 2o0j 2o0k
17373706 W.Zheng, J.C.Liao, B.R.Brooks, and S.Doniach (2007).
Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model.
  Proteins, 67, 886-896.  
17003052 C.Ioannou, P.M.Schaeffer, N.E.Dixon, and P.Soultanas (2006).
Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading in Bacillus subtilis.
  Nucleic Acids Res, 34, 5247-5258.  
16258174 M.S.Mitchell, and V.B.Rao (2006).
Functional analysis of the bacteriophage T4 DNA-packaging ATPase motor.
  J Biol Chem, 281, 518-527.  
16340008 M.C.Zittel, and J.L.Keck (2005).
Coupling DNA-binding and ATP hydrolysis in Escherichia coli RecQ: role of a highly conserved aromatic-rich sequence.
  Nucleic Acids Res, 33, 6982-6991.  
16041061 M.S.Dillingham, M.R.Webb, and S.C.Kowalczykowski (2005).
Bipolar DNA translocation contributes to highly processive DNA unwinding by RecBCD enzyme.
  J Biol Chem, 280, 37069-37077.  
16041060 M.Spies, M.S.Dillingham, and S.C.Kowalczykowski (2005).
Translocation by the RecB motor is an absolute requirement for {chi}-recognition and RecA protein loading by RecBCD enzyme.
  J Biol Chem, 280, 37078-37087.  
15528191 N.L.Korneeva, E.A.First, C.A.Benoit, and R.E.Rhoads (2005).
Interaction between the NH2-terminal domain of eIF4A and the central domain of eIF4G modulates RNA-stimulated ATPase activity.
  J Biol Chem, 280, 1872-1881.  
15855170 S.Kuusk, T.Sedman, P.Jõers, and J.Sedman (2005).
Hmi1p from Saccharomyces cerevisiae mitochondria is a structure-specific DNA helicase.
  J Biol Chem, 280, 24322-24329.  
15070725 D.J.Crampton, S.Guo, D.E.Johnson, and C.C.Richardson (2004).
The arginine finger of bacteriophage T7 gene 4 helicase: role in energy coupling.
  Proc Natl Acad Sci U S A, 101, 4373-4378.  
15479787 D.N.Frick, R.S.Rypma, A.M.Lam, and C.M.Frenz (2004).
Electrostatic analysis of the hepatitis C virus NS3 helicase reveals both active and allosteric site locations.
  Nucleic Acids Res, 32, 5519-5528.  
15310852 J.A.James, A.K.Aggarwal, R.M.Linden, and C.R.Escalante (2004).
Structure of adeno-associated virus type 2 Rep40-ADP complex: insight into nucleotide recognition and catalysis by superfamily 3 helicases.
  Proc Natl Acad Sci U S A, 101, 12455-12460.
PDB code: 1u0j
15140959 K.A.Ivanov, V.Thiel, J.C.Dobbe, Y.van der Meer, E.J.Snijder, and J.Ziebuhr (2004).
Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase.
  J Virol, 78, 5619-5632.  
14512529 A.C.Vlot, S.M.Laros, and J.F.Bol (2003).
Coordinate replication of alfalfa mosaic virus RNAs 1 and 2 involves cis- and trans-acting functions of the encoded helicase-like and polymerase-like domains.
  J Virol, 77, 10790-10798.  
12458209 R.J.Bienstock, M.Skorvaga, B.S.Mandavilli, and B.Van Houten (2003).
Structural and functional characterization of the human DNA repair helicase XPD by comparative molecular modeling and site-directed mutagenesis of the bacterial repair protein UvrB.
  J Biol Chem, 278, 5309-5316.  
11823434 A.C.Rodríguez, and D.Stock (2002).
Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA.
  EMBO J, 21, 418-426.
PDB codes: 1gku 1gl9
11839499 J.M.Caruthers, and D.B.McKay (2002).
Helicase structure and mechanism.
  Curr Opin Struct Biol, 12, 123-133.  
12065426 M.A.Petit, and D.Ehrlich (2002).
Essential bacterial helicases that counteract the toxicity of recombination proteins.
  EMBO J, 21, 3137-3147.  
11781105 M.S.Dillingham, D.B.Wigley, and M.R.Webb (2002).
Direct measurement of single-stranded DNA translocation by PcrA helicase using the fluorescent base analogue 2-aminopurine.
  Biochemistry, 41, 643-651.  
12209147 P.Chène (2002).
ATPases as drug targets: learning from their structure.
  Nat Rev Drug Discov, 1, 665-673.  
11842108 P.Soultanas (2002).
A functional interaction between the putative primosomal protein DnaI and the main replicative DNA helicase DnaB in Bacillus.
  Nucleic Acids Res, 30, 966-974.  
12235389 P.Soultanas, and D.B.Wigley (2002).
Site-directed mutagenesis reveals roles for conserved amino acid residues in the hexameric DNA helicase DnaB from Bacillus stearothermophilus.
  Nucleic Acids Res, 30, 4051-4060.  
11350034 C.A.Tsu, K.Kossen, and O.C.Uhlenbeck (2001).
The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA.
  RNA, 7, 702-709.  
11551790 C.Geourjon, C.Orelle, E.Steinfels, C.Blanchet, G.Deléage, A.Di Pietro, and J.M.Jault (2001).
A common mechanism for ATP hydrolysis in ABC transporter and helicase superfamilies.
  Trends Biochem Sci, 26, 539-544.  
11459979 M.S.Dillingham, P.Soultanas, P.Wiley, M.R.Webb, and D.B.Wigley (2001).
Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase.
  Proc Natl Acad Sci U S A, 98, 8381-8387.  
10917600 A.Seybert, A.Hegyi, S.G.Siddell, and J.Ziebuhr (2000).
The human coronavirus 229E superfamily 1 helicase has RNA and DNA duplex-unwinding activities with 5'-to-3' polarity.
  RNA, 6, 1056-1068.  
11000230 A.Seybert, L.C.van Dinten, E.J.Snijder, and J.Ziebuhr (2000).
Biochemical characterization of the equine arteritis virus helicase suggests a close functional relationship between arterivirus and coronavirus helicases.
  J Virol, 74, 9586-9593.  
10820025 C.L.Booth, L.Pulaski, M.M.Gottesman, and I.Pastan (2000).
Analysis of the properties of the N-terminal nucleotide-binding domain of human P-glycoprotein.
  Biochemistry, 39, 5518-5526.  
11087862 J.M.Caruthers, E.R.Johnson, and D.B.McKay (2000).
Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase.
  Proc Natl Acad Sci U S A, 97, 13080-13085.
PDB codes: 1fuk 1fuu
10892646 M.R.Singleton, M.R.Sawaya, T.Ellenberger, and D.B.Wigley (2000).
Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides.
  Cell, 101, 589-600.
PDB codes: 1e0j 1e0k
10679457 P.Soultanas, and D.B.Wigley (2000).
DNA helicases: 'inching forward'.
  Curr Opin Struct Biol, 10, 124-128.  
10899133 P.Soultanas, M.S.Dillingham, P.Wiley, M.R.Webb, and D.B.Wigley (2000).
Uncoupling DNA translocation and helicase activity in PcrA: direct evidence for an active mechanism.
  EMBO J, 19, 3799-3810.  
10944338 S.P.Prewitt, A.A.Komissarov, S.L.Deutscher, and J.J.Tanner (2000).
Crystallization and molecular-replacement studies of a recombinant antigen-binding fragment complexed with single-stranded DNA.
  Acta Crystallogr D Biol Crystallogr, 56, 1007-1011.  
10601012 K.Theis, P.J.Chen, M.Skorvaga, B.Van Houten, and C.Kisker (1999).
Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair.
  EMBO J, 18, 6899-6907.
PDB codes: 1d9x 1d9z
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.