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PDBsum entry 1zio

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protein ligands metals links
Transferase PDB id
1zio
Jmol
Contents
Protein chain
217 a.a. *
Ligands
AP5
Metals
_ZN
_MG
Waters ×203
* Residue conservation analysis
PDB id:
1zio
Name: Transferase
Title: Phosphotransferase
Structure: Adenylate kinase. Chain: a. Synonym: adk. Other_details: zinc finger
Source: Geobacillus stearothermophilus. Organism_taxid: 1422
Resolution:
1.96Å     R-factor:   0.161     R-free:   0.228
Authors: M.B.Berry,G.N.Phillips Jr.
Key ref: M.B.Berry and G.N.Phillips (1998). Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+. Proteins, 32, 276-288. PubMed id: 9715904
Date:
07-Jun-96     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P27142  (KAD_GEOSE) -  Adenylate kinase
Seq:
Struc:
217 a.a.
217 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.4.3  - Adenylate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + AMP = 2 ADP
ATP
Bound ligand (Het Group name = AP5)
matches with 54.00% similarity
+ AMP
= 2 × ADP
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     AMP salvage   5 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    reference    
 
 
Proteins 32:276-288 (1998)
PubMed id: 9715904  
 
 
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.
M.B.Berry, G.N.Phillips.
 
  ABSTRACT  
 
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mn2+ Ap5A, and Mg2+ Ap5A have been determined by X-ray crystallography to resolutions of 1.6 A, 1.85 A, and 1.96 A, respectively. The protein's lid domain is partially open, being both rotated and translated away from bound Ap5A. The flexibility of the lid domain in the ternary state and its ability to transfer force directly to the the active site is discussed in light of our proposed entropic mechanism for catalytic turnover. The bound Zn2+ atom is demonstrably structural in nature, with no contacts other than its ligating cysteine residues within 5 A. The B. stearothermophilus adenylate kinase lid appears to be a truncated zinc finger domain, lacking the DNA binding finger, which we have termed a zinc knuckle domain. In the Mg2+ Ap5A and Mn2+ Ap5A structures, Mg2+ and Mn2+ demonstrate six coordinate octahedral geometry. The interactions of the Mg2+-coordinated water molecules with the protein and Ap5A phosphate chain demonstrate their involvement in catalyzing phosphate transfer. The protein selects for beta-y (preferred by Mg2+) rather than alpha-gamma (preferred by Mn2+) metal ion coordination by forcing the ATP phosphate chain to have an extended conformation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20821240 A.Mukhopadhyay, A.V.Kladova, S.A.Bursakov, O.Y.Gavel, J.J.Calvete, V.L.Shnyrov, I.Moura, J.J.Moura, M.J.Romão, and J.Trincão (2011).
Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria.
  J Biol Inorg Chem, 16, 51-61.
PDB codes: 2xb4 3l0p 3l0s
20714505 N.Stern, D.T.Major, H.E.Gottlieb, D.Weizman, and B.Fischer (2010).
What is the conformation of physiologically-active dinucleoside polyphosphates in solution? Conformational analysis of free dinucleoside polyphosphates by NMR and molecular dynamics simulations.
  Org Biomol Chem, 8, 4637-4652.  
19217394 A.R.Kinjo, and H.Nakamura (2009).
Comprehensive structural classification of ligand-binding motifs in proteins.
  Structure, 17, 234-246.  
19381696 F.Luttringer, E.Mulliez, B.Dublet, D.Lemaire, and M.Fontecave (2009).
The Zn center of the anaerobic ribonucleotide reductase from E. coli.
  J Biol Inorg Chem, 14, 923-933.  
19751742 O.Beckstein, E.J.Denning, J.R.Perilla, and T.B.Woolf (2009).
Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.
  J Mol Biol, 394, 160-176.  
19130895 R.Liu, A.L.Ström, J.Zhai, J.Gal, S.Bao, W.Gong, and H.Zhu (2009).
Enzymatically inactive adenylate kinase 4 interacts with mitochondrial ADP/ATP translocase.
  Int J Biochem Cell Biol, 41, 1371-1380.  
19029291 Y.W.Tan, J.A.Hanson, and H.Yang (2009).
Direct Mg2+ Binding Activates Adenylate Kinase from Escherichia coli.
  J Biol Chem, 284, 3306-3313.  
17680690 D.A.Kondrashov, W.Zhang, R.Aranda, B.Stec, and G.N.Phillips (2008).
Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments.
  Proteins, 70, 353-362.
PDB codes: 1jw8 1u7r 1u7s
18174226 R.L.Sherrer, P.O'Donoghue, and D.Söll (2008).
Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation.
  Nucleic Acids Res, 36, 1247-1259.  
17039546 N.Nagano, T.Noguchi, and Y.Akiyama (2007).
Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.
  Proteins, 66, 147-159.  
17914902 W.Tempel, W.M.Rabeh, K.L.Bogan, P.Belenky, M.Wojcik, H.F.Seidle, L.Nedyalkova, T.Yang, A.A.Sauve, H.W.Park, and C.Brenner (2007).
Nicotinamide riboside kinase structures reveal new pathways to NAD+.
  PLoS Biol, 5, e263.
PDB codes: 2p0e 2qsy 2qsz 2qt0 2qt1
17419878 Y.Wei, J.Ko, L.F.Murga, and M.J.Ondrechen (2007).
Selective prediction of interaction sites in protein structures with THEMATICS.
  BMC Bioinformatics, 8, 119.  
16361259 C.H.Gross, N.Abdul-Manan, J.Fulghum, J.Lippke, X.Liu, P.Prabhakar, D.Brennan, M.S.Willis, C.Faerman, P.Connelly, S.Raybuck, and J.Moore (2006).
Nucleotide-binding domains of cystic fibrosis transmembrane conductance regulator, an ABC transporter, catalyze adenylate kinase activity but not ATP hydrolysis.
  J Biol Chem, 281, 4058-4068.  
16500903 G.Zhao, X.Zhou, L.Wang, G.Li, C.Kisker, W.J.Lennarz, and H.Schindelin (2006).
Structure of the mouse peptide N-glycanase-HR23 complex suggests co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways.
  J Biol Chem, 281, 13751-13761.
PDB codes: 2f4m 2f4o
16672241 M.Bellinzoni, A.Haouz, M.Graña, H.Munier-Lehmann, W.Shepard, and P.M.Alzari (2006).
The crystal structure of Mycobacterium tuberculosis adenylate kinase in complex with two molecules of ADP and Mg2+ supports an associative mechanism for phosphoryl transfer.
  Protein Sci, 15, 1489-1493.
PDB code: 2cdn
16214343 A.Gutteridge, and J.M.Thornton (2005).
Understanding nature's catalytic toolkit.
  Trends Biochem Sci, 30, 622-629.  
16021631 G.Hernández, and D.M.LeMaster (2005).
Hybrid native partitioning of interactions among nonconserved residues in chimeric proteins.
  Proteins, 60, 723-731.  
15521058 H.Krishnamurthy, H.Lou, A.Kimple, C.Vieille, and R.I.Cukier (2005).
Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates.
  Proteins, 58, 88.  
15995219 P.A.Videira, A.P.Garcia, and I.Sá-Correia (2005).
Functional and topological analysis of the Burkholderia cenocepacia priming glucosyltransferase BceB, involved in the biosynthesis of the cepacian exopolysaccharide.
  J Bacteriol, 187, 5013-5018.  
14997573 I.L.de La Sierra-Gallay, B.Collinet, M.Graille, S.Quevillon-Cheruel, D.Liger, P.Minard, K.Blondeau, G.Henckes, R.Aufrère, N.Leulliot, C.Z.Zhou, I.Sorel, J.L.Ferrer, A.Poupon, J.Janin, and H.van Tilbeurgh (2004).
Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase.
  Proteins, 54, 776-783.
PDB code: 1odf
15130468 N.N.Suzuki, K.Koizumi, M.Fukushima, A.Matsuda, and F.Inagaki (2004).
Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase.
  Structure, 12, 751-764.
PDB codes: 1udw 1uei 1uej 1ufq 1uj2
12571357 A.Meinhart, J.C.Alonso, N.Sträter, and W.Saenger (2003).
Crystal structure of the plasmid maintenance system epsilon/zeta: functional mechanism of toxin zeta and inactivation by epsilon 2 zeta 2 complex formation.
  Proc Natl Acad Sci U S A, 100, 1661-1666.
PDB code: 1gvn
14622299 H.Villa, Y.Pérez-Pertejo, C.García-Estrada, R.M.Reguera, J.M.Requena, B.L.Tekwani, R.Balaña-Fouce, and D.Ordóñez (2003).
Molecular and functional characterization of adenylate kinase 2 gene from Leishmania donovani.
  Eur J Biochem, 270, 4339-4347.  
12538896 N.O'Toole, J.A.Barbosa, Y.Li, L.W.Hung, A.Matte, and M.Cygler (2003).
Crystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli.
  Protein Sci, 12, 327-336.
PDB code: 1n3b
12527760 S.S.Krishna, I.Majumdar, and N.V.Grishin (2003).
Structural classification of zinc fingers: survey and summary.
  Nucleic Acids Res, 31, 532-550.  
12093921 E.E.Fetsch, and A.L.Davidson (2002).
Vanadate-catalyzed photocleavage of the signature motif of an ATP-binding cassette (ABC) transporter.
  Proc Natl Acad Sci U S A, 99, 9685-9690.  
12110598 L.K.Wang, C.D.Lima, and S.Shuman (2002).
Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme.
  EMBO J, 21, 3873-3880.
PDB code: 1ly1
11842120 L.K.Wang, and S.Shuman (2002).
Mutational analysis defines the 5'-kinase and 3'-phosphatase active sites of T4 polynucleotide kinase.
  Nucleic Acids Res, 30, 1073-1080.  
11483495 S.Fieulaine, S.Morera, S.Poncet, V.Monedero, V.Gueguen-Chaignon, A.Galinier, J.Janin, J.Deutscher, and S.Nessler (2001).
X-ray structure of HPr kinase: a bacterial protein kinase with a P-loop nucleotide-binding domain.
  EMBO J, 20, 3917-3927.
PDB code: 1jb1
11325743 S.Kumar, Y.Y.Sham, C.J.Tsai, and R.Nussinov (2001).
Protein folding and function: the N-terminal fragment in adenylate kinase.
  Biophys J, 80, 2439-2454.  
10835366 T.Izard, and J.Ellis (2000).
The crystal structures of chloramphenicol phosphotransferase reveal a novel inactivation mechanism.
  EMBO J, 19, 2690-2700.
PDB codes: 1qhn 1qhs 1qhx 1qhy
10099128 P.J.O'Brien, and D.Herschlag (1999).
Catalytic promiscuity and the evolution of new enzymatic activities.
  Chem Biol, 6, R91.  
9875848 C.S.Raman, H.Li, P.Martásek, V.Král, B.S.Masters, and T.L.Poulos (1998).
Crystal structure of constitutive endothelial nitric oxide synthase: a paradigm for pterin function involving a novel metal center.
  Cell, 95, 939-950.
PDB codes: 1nse 2nse 3nse 4nse
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.