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PDBsum entry 1gky

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Transferase PDB id
1gky
Jmol
Contents
Protein chain
187 a.a. *
Ligands
SO4
5GP
Waters ×173
* Residue conservation analysis
PDB id:
1gky
Name: Transferase
Title: Refined structure of the complex between guanylate kinase and its substrate gmp at 2.0 angstroms resolution
Structure: Guanylate kinase. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.173    
Authors: T.Stehle,G.E.Schulz
Key ref:
T.Stehle and G.E.Schulz (1992). Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 A resolution. J Mol Biol, 224, 1127-1141. PubMed id: 1314905 DOI: 10.1016/0022-2836(92)90474-X
Date:
23-Dec-91     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15454  (KGUA_YEAST) -  Guanylate kinase
Seq:
Struc:
187 a.a.
186 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.4.8  - Guanylate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + GMP = ADP + GDP
ATP
+
GMP
Bound ligand (Het Group name = 5GP)
corresponds exactly
= ADP
+ GDP
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   4 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0022-2836(92)90474-X J Mol Biol 224:1127-1141 (1992)
PubMed id: 1314905  
 
 
Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 A resolution.
T.Stehle, G.E.Schulz.
 
  ABSTRACT  
 
The crystal structure of guanylate kinase from Saccharomyces cerevisiae complexed with its substrate GMP has been refined at a resolution of 2.0 A. The final crystallographic R-factor is 17.3% in the resolution range 7.0 A to 2.0 A for all reflections of the 100% complete data set. The final model has standard geometry with root-mean-square deviations of 0.016 A in bond lengths and 3.0 in bond angles. It consists of all 186 amino acid residues, the N-terminal acetyl group, the substrate GMP, one sulfate ion and 174 water molecules. Guanylate kinase is structurally related to adenylate kinases and G-proteins with respect to its central beta-sheet with connecting helices and the giant anion hole that binds nucleoside triphosphates. These nucleotides are ATP and GTP for the kinases and GTP for the G-proteins. The chain segment binding the substrate GMP of guanylate kinase differs grossly from the respective part of the adenylate kinases; it has no counterpart in the G-proteins. The binding mode of GMP is described in detail. Probably, the observed structure represents one of several structurally quite different intermediate states of the catalytic cycle.
 
  Selected figure(s)  
 
Figure 9.
Figure 9. Superposition of the C'' backbones of GK (thick line) with AK1 of Dreusicke et al. (1988) as oalculated with program OVERLAY (Kabsch, 1978) using a cut-off of 3 A. The equivalenced 103 C'' atoms of GK are 1 to 24, 29 to 32,81 to 91,93 to 99,105, 109, 113 to 122, 124 to 132, 139 to 149, 151, 152 and 163 to 185. The corresponding residues of AK1 can be taken from Fig. 4.
Figure 14.
Figure 14. Stereo view of the interactions between the sulfate ion and GK, showing the sulfate ion, residues Gly8- Pro9-SerlO-Glyl1-Thr12-Gly13-Lys14-Serl5, and the guanidinium group of Arg135.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 224, 1127-1141) copyright 1992.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21081090 S.Sacquin-Mora, O.Delalande, and M.Baaden (2010).
Functional modes and residue flexibility control the anisotropic response of guanylate kinase to mechanical stress.
  Biophys J, 99, 3412-3419.  
19136674 A.Ardiani, A.Goyke, and M.E.Black (2009).
Mutations at serine 37 in mouse guanylate kinase confer resistance to 6-thioguanine.
  Protein Eng Des Sel, 22, 225-232.  
19419194 B.D.Ray, J.Scott, H.Yan, and B.D.Rao (2009).
Productive versus unproductive nucleotide binding in yeast guanylate kinase mutants: comparison of R41M with K14M by proton two dimensional transferred NOESY.
  Biochemistry, 48, 5532-5540.  
18343960 R.A.Caceres, L.F.Macedo Timmers, A.L.Vivan, C.Z.Schneider, L.A.Basso, W.F.De Azevedo, and D.S.Santos (2008).
Molecular modeling and dynamics studies of cytidylate kinase from Mycobacterium tuberculosis H37Rv.
  J Mol Model, 14, 427-434.  
17678554 A.J.te Velthuis, J.F.Admiraal, and C.P.Bagowski (2007).
Molecular evolution of the MAGUK family in metazoan genomes.
  BMC Evol Biol, 7, 129.  
17698003 J.A.Khan, S.Xiang, and L.Tong (2007).
Crystal structure of human nicotinamide riboside kinase.
  Structure, 15, 1005-1013.
PDB codes: 2qg6 2ql6
17303572 P.Béguin, Y.J.Ng, C.Krause, R.N.Mahalakshmi, M.Y.Ng, and W.Hunziker (2007).
RGK small GTP-binding proteins interact with the nucleotide kinase domain of Ca2+-channel beta-subunits via an uncommon effector binding domain.
  J Biol Chem, 282, 11509-11520.  
17292915 W.Xie, C.Zhou, and R.H.Huang (2007).
Structure of tRNA dimethylallyltransferase: RNA modification through a channel.
  J Mol Biol, 367, 872-881.
PDB codes: 3crm 3crq 3crr
  16880539 B.Dhaliwal, J.Ren, M.Lockyer, I.Charles, A.R.Hawkins, and D.K.Stammers (2006).
Structure of Staphylococcus aureus cytidine monophosphate kinase in complex with cytidine 5'-monophosphate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 710-715.
PDB code: 2h92
16288457 G.Hible, P.Christova, L.Renault, E.Seclaman, A.Thompson, E.Girard, H.Munier-Lehmann, and J.Cherfils (2006).
Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase.
  Proteins, 62, 489-500.
PDB codes: 1znw 1znx 1zny 1znz
  17012781 K.El Omari, B.Dhaliwal, M.Lockyer, I.Charles, A.R.Hawkins, and D.K.Stammers (2006).
Structure of Staphylococcus aureus guanylate monophosphate kinase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 949-953.
PDB code: 2j41
15843420 C.L.Noble, E.R.Nimmo, H.Drummond, L.Smith, I.D.Arnott, and J.Satsangi (2005).
DLG5 variants do not influence susceptibility to inflammatory bowel disease in the Scottish population.
  Gut, 54, 1416-1420.  
15134636 Y.Opatowsky, C.C.Chen, K.P.Campbell, and J.A.Hirsch (2004).
Structural analysis of the voltage-dependent calcium channel beta subunit functional core and its complex with the alpha 1 interaction domain.
  Neuron, 42, 387-399.
PDB codes: 1t3l 1t3s
14594851 B.J.Beck, M.Huelsmeyer, S.Paul, and D.M.Downs (2003).
A mutation in the essential gene gmk (encoding guanlyate kinase) generates a requirement for adenine at low temperature in Salmonella enterica.
  J Bacteriol, 185, 6732-6735.  
12414806 B.Singh, and N.B.Schwartz (2003).
Identification and functional characterization of the novel BM-motif in the murine phosphoadenosine phosphosulfate (PAPS) synthetase.
  J Biol Chem, 278, 71-75.  
12482754 O.Olsen, and D.S.Bredt (2003).
Functional analysis of the nucleotide binding domain of membrane-associated guanylate kinases.
  J Biol Chem, 278, 6873-6878.  
  11876824 G.Shah, R.Brugada, O.Gonzalez, G.Czernuszewicz, R.A.Gibbs, L.Bachinski, and R.Roberts (2002).
The cloning, genomic organization and tissue expression profile of the human DLG5 gene.
  BMC Genomics, 3, 6.  
12036965 N.Sekulic, L.Shuvalova, O.Spangenberg, M.Konrad, and A.Lavie (2002).
Structural characterization of the closed conformation of mouse guanylate kinase.
  J Biol Chem, 277, 30236-30243.
PDB code: 1lvg
11779504 A.W.McGee, S.R.Dakoji, O.Olsen, D.S.Bredt, W.A.Lim, and K.E.Prehoda (2001).
Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins.
  Mol Cell, 8, 1291-1301.
PDB code: 1kjw
11717264 V.Chazalet, K.Uehara, R.A.Geremia, and C.Breton (2001).
Identification of essential amino acids in the Azorhizobium caulinodans fucosyltransferase NodZ.
  J Bacteriol, 183, 7067-7075.  
11060025 H.Wu, C.Reissner, S.Kuhlendahl, B.Coblentz, S.Reuver, S.Kindler, E.D.Gundelfinger, and C.C.Garner (2000).
Intramolecular interactions regulate SAP97 binding to GKAP.
  EMBO J, 19, 5740-5751.  
10677210 I.J.MacRae, I.H.Segel, and A.J.Fisher (2000).
Crystal structure of adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum.
  Biochemistry, 39, 1613-1621.
PDB code: 1d6j
11123913 I.M.Li de La Sierra, J.Gallay, M.Vincent, T.Bertrand, P.Briozzo, O.Bârzu, and A.M.Gilles (2000).
Substrate-induced fit of the ATP binding site of cytidine monophosphate kinase from Escherichia coli: time-resolved fluorescence of 3'-anthraniloyl-2'-deoxy-ADP and molecular modeling.
  Biochemistry, 39, 15870-15878.  
10891066 N.Campobasso, I.I.Mathews, T.P.Begley, and S.E.Ealick (2000).
Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.
  Biochemistry, 39, 7868-7877.
PDB codes: 1c3q 1ekk 1ekq 1esj 1esq
10632732 V.Kumar, O.Spangenberg, and M.Konrad (2000).
Cloning of the guanylate kinase homologues AGK-1 and AGK-2 from Arabidopsis thaliana and characterization of AGK-1.
  Eur J Biochem, 267, 606-615.  
10585400 H.Prinz, A.Lavie, A.J.Scheidig, O.Spangenberg, and M.Konrad (1999).
Binding of nucleotides to guanylate kinase, p21(ras), and nucleoside-diphosphate kinase studied by nano-electrospray mass spectrometry.
  J Biol Chem, 274, 35337-35342.  
10026200 N.Masuko, K.Makino, H.Kuwahara, K.Fukunaga, T.Sudo, N.Araki, H.Yamamoto, Y.Yamada, E.Miyamoto, and H.Saya (1999).
Interaction of NE-dlg/SAP102, a neuronal and endocrine tissue-specific membrane-associated guanylate kinase protein, with calmodulin and PSD-95/SAP90. A possible regulatory role in molecular clustering at synaptic sites.
  J Biol Chem, 274, 5782-5790.  
9660868 A.R.Cohen, D.F.Woods, S.M.Marfatia, Z.Walther, A.H.Chishti, J.M.Anderson, and D.F.Wood (1998).
Human CASK/LIN-2 binds syndecan-2 and protein 4.1 and localizes to the basolateral membrane of epithelial cells.
  J Cell Biol, 142, 129-138.  
9548738 D.H.Harrison, J.A.Runquist, A.Holub, and H.M.Miziorko (1998).
The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase.
  Biochemistry, 37, 5074-5085.
PDB code: 1a7j
9843365 I.I.Mathews, M.D.Erion, and S.E.Ealick (1998).
Structure of human adenosine kinase at 1.5 A resolution.
  Biochemistry, 37, 15607-15620.
PDB code: 1bx4
9862805 P.Briozzo, B.Golinelli-Pimpaneau, A.M.Gilles, J.F.Gaucher, S.Burlacu-Miron, H.Sakamoto, J.Janin, and O.Bârzu (1998).
Structures of escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity.
  Structure, 6, 1517-1527.
PDB codes: 1cke 2cmk
9360604 Y.Kakuta, L.G.Pedersen, C.W.Carter, M.Negishi, and L.C.Pedersen (1997).
Crystal structure of estrogen sulphotransferase.
  Nat Struct Biol, 4, 904-908.
PDB codes: 1aqu 1aqy
9235932 Y.Zhang, Y.Li, Y.Wu, and H.Yan (1997).
Structural and functional roles of tyrosine 78 of yeast guanylate kinase.
  J Biol Chem, 272, 19343-19350.  
  8670851 A.Teplyakov, P.Sebastiao, G.Obmolova, A.Perrakis, G.S.Brush, M.J.Bessman, and K.S.Wilson (1996).
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
  EMBO J, 15, 3487-3497.
PDB codes: 1dek 1del
8785318 C.A.Smith, and I.Rayment (1996).
Active site comparisons highlight structural similarities between myosin and other P-loop proteins.
  Biophys J, 70, 1590-1602.  
8805521 C.W.Müller, G.J.Schlauderer, J.Reinstein, and G.E.Schulz (1996).
Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding.
  Structure, 4, 147-156.
PDB code: 4ake
8830775 D.F.Woods, C.Hough, D.Peel, G.Callaini, and P.J.Bryant (1996).
Dlg protein is required for junction structure, cell polarity, and proliferation control in Drosophila epithelia.
  J Cell Biol, 134, 1469-1482.  
  8868479 G.J.Schlauderer, and G.E.Schulz (1996).
The structure of bovine mitochondrial adenylate kinase: comparison with isoenzymes in other compartments.
  Protein Sci, 5, 434-441.
PDB codes: 1ak2 2ak2
8703943 K.Scheffzek, W.Kliche, L.Wiesmüller, and J.Reinstein (1996).
Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity.
  Biochemistry, 35, 9716-9727.
PDB codes: 1ukd 1uke
8663313 W.A.Brady, M.S.Kokoris, M.Fitzgibbon, and M.E.Black (1996).
Cloning, characterization, and modeling of mouse and human guanylate kinases.
  J Biol Chem, 271, 16734-16740.  
8910414 Y.Li, Y.Zhang, and H.Yan (1996).
Kinetic and thermodynamic characterizations of yeast guanylate kinase.
  J Biol Chem, 271, 28038-28044.  
8789193 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 2. Influence of local site surface shape on water binding.
  J Comput Aided Mol Des, 9, 513-520.  
8026505 E.Schiltz, S.Burger, R.Grafmüller, W.R.Deppert, W.Haehnel, and E.Wagner (1994).
Primary structure of maize chloroplast adenylate kinase.
  Eur J Biochem, 222, 949-954.  
7937897 R.A.Lue, S.M.Marfatia, D.Branton, and A.H.Chishti (1994).
Cloning and characterization of hdlg: the human homologue of the Drosophila discs large tumor suppressor binds to protein 4.1.
  Proc Natl Acad Sci U S A, 91, 9818-9822.  
8035212 S.D.Rufino, and T.L.Blundell (1994).
Structure-based identification and clustering of protein families and superfamilies.
  J Comput Aided Mol Des, 8, 5.  
8097461 P.D.Zschocke, E.Schiltz, and G.E.Schulz (1993).
Purification and sequence determination of guanylate kinase from pig brain.
  Eur J Biochem, 213, 263-269.  
1338911 E.V.Koonin, D.F.Woods, and P.J.Bryant (1992).
dlg-R proteins: modified guanylate kinases.
  Nat Genet, 2, 256-257.  
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.