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PDBsum entry 1jq3

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1jq3
Jmol
Contents
Protein chains
295 a.a. *
Ligands
AAT ×3
Waters ×743
* Residue conservation analysis
PDB id:
1jq3
Name: Transferase
Title: Crystal structure of spermidine synthase in complex with transition state analogue adodato
Structure: Spermidine synthase. Chain: a, b, c, d. Synonym: putrescine aminopropyltransferase, spdsy. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.80Å     R-factor:   0.196     R-free:   0.229
Authors: S.Korolev,Y.Ikeguchi,T.Skarina,S.Beasley,A.Edwards, A.Joachimiak,A.E.Pegg,A.Savchenko,Midwest Center For Structural Genomics (Mcsg)
Key ref:
S.Korolev et al. (2002). The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat Struct Biol, 9, 27-31. PubMed id: 11731804 DOI: 10.1038/nsb737
Date:
03-Aug-01     Release date:   21-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9WZC2  (SPEE_THEMA) -  Polyamine aminopropyl transferase
Seq:
Struc:
296 a.a.
295 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.5.1.16  - Spermidine synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Spermine Biosynthesis
      Reaction: S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl- 5'-thioadenosine + spermidine
S-adenosyl 3-(methylthio)propylamine
Bound ligand (Het Group name = AAT)
matches with 76.00% similarity
+ putrescine
= 5'-S-methyl- 5'-thioadenosine
+ spermidine
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     polyamine biosynthetic process   2 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    Added reference    
 
 
DOI no: 10.1038/nsb737 Nat Struct Biol 9:27-31 (2002)
PubMed id: 11731804  
 
 
The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor.
S.Korolev, Y.Ikeguchi, T.Skarina, S.Beasley, C.Arrowsmith, A.Edwards, A.Joachimiak, A.E.Pegg, A.Savchenko.
 
  ABSTRACT  
 
Polyamines are essential in all branches of life. Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the biosynthesis of spermidine, a ubiquitous polyamine. The crystal structure of the PAPT from Thermotoga maritima (TmPAPT) has been solved to 1.5 A resolution in the presence and absence of AdoDATO (S-adenosyl-1,8-diamino-3-thiooctane), a compound containing both substrate and product moieties. This, the first structure of an aminopropyltransferase, reveals deep cavities for binding substrate and cofactor, and a loop that envelops the active site. The AdoDATO binding site is lined with residues conserved in PAPT enzymes from bacteria to humans, suggesting a universal catalytic mechanism. Other conserved residues act sterically to provide a structural basis for polyamine specificity. The enzyme is tetrameric; each monomer consists of a C-terminal domain with a Rossmann-like fold and an N-terminal beta-stranded domain. The tetramer is assembled using a novel barrel-type oligomerization motif.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. General pathway for the biosynthesis of putrescine, spermidine and spermine.
Figure 4.
Figure 4. Interaction of AdoDATO with TmPAPT. a, A stereo view of F[o] - F[c] electron density map produced by omitting the AdoDATO from the model during simulated annealing refinement and map calculation, and contoured at 2.0 level around AdoDATO bound to subunit D (generated with O24). b, Close-up stereo view of substrate binding site. The view is shown from the N-terminal domain toward the C-terminal domain. AdoDATO and selected residues involved in inhibitor binding are shown in stick representation. Nitrogens, oxygens and sulfurs are shown in blue, red and yellow, respectively. Carbons of TmPAPT residues are shown in gray, and carbons of AdoDATO are shown in cyan. The water molecule is shown as an orange sphere. Hydrogen bonds are shown by thin black lines. The C-terminal domain is shown in light yellow transparent ribbon representation. The gatekeeping loop is shown by green worm representation and the corresponding loop of subunit C by transparent blue worm representation. The C11 group of AdoDATO corresponding to attacking amino group of putrescine is highlighted by magenta. The proposed hydrogen bond involved in deprotonation of the corresponding amino group of putrescine is shown by a magenta line. c, Schematic LIGPLOT29 diagram of the interactions between AdoDATO (bonds shown in violet) and TmPAPT. Protein side chains that form hydrogen bonds with AdoDATO are shown with bonds in orange. Hydrogen bonds are drawn as dashed lines, and the donor-acceptor distances are given. Residues involved in hydrophobic interactions are shown with arcs. Residue names and numbers are highlighted by colors corresponding to colors on structural alignment picture (Fig. 3).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 27-31) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21458463 M.Ohnuma, T.Ganbe, Y.Terui, M.Niitsu, T.Sato, N.Tanaka, M.Tamakoshi, K.Samejima, T.Kumasaka, and T.Oshima (2011).
Crystal structures and enzymatic properties of a triamine/agmatine aminopropyltransferase from Thermus thermophilus.
  J Mol Biol, 408, 971-986.
PDB codes: 1uir 3anx
19859664 A.E.Pegg, and A.J.Michael (2010).
Spermine synthase.
  Cell Mol Life Sci, 67, 113-121.  
20372740 D.O'Hagan, and J.W.Schmidberger (2010).
Enzymes that catalyse SN2 reaction mechanisms.
  Nat Prod Rep, 27, 900-918.  
20194791 D.S.Auld, S.Lovell, N.Thorne, W.A.Lea, D.J.Maloney, M.Shen, G.Rai, K.P.Battaile, C.J.Thomas, A.Simeonov, R.P.Hanzlik, and J.Inglese (2010).
Molecular basis for the high-affinity binding and stabilization of firefly luciferase by PTC124.
  Proc Natl Acad Sci U S A, 107, 4878-4883.
PDB codes: 3iep 3ier 3ies
20532909 M.C.Gomez-Jimenez, M.A.Paredes, M.Gallardo, N.Fernandez-Garcia, E.Olmos, and I.M.Sanchez-Calle (2010).
Tissue-specific expression of olive S-adenosyl methionine decarboxylase and spermidine synthase genes and polyamine metabolism during flower opening and early fruit development.
  Planta, 232, 629-647.  
20336313 M.Trénor, M.A.Perez-Amador, J.Carbonell, and M.A.Blázquez (2010).
Expression of polyamine biosynthesis genes during parthenocarpic fruit development in Citrus clementina.
  Planta, 231, 1401-1411.  
20067992 S.Kametaka, N.Sawada, J.S.Bonifacino, and S.Waguri (2010).
Functional characterization of protein-sorting machineries at the trans-Golgi network in Drosophila melanogaster.
  J Cell Sci, 123, 460-471.  
19685160 S.Parvin, Y.J.Kim, R.K.Pulla, S.Sathiyamoorthy, M.G.Miah, Y.J.Kim, N.G.Wasnik, and D.C.Yang (2010).
Identification and characterization of spermidine synthase gene from Panax ginseng.
  Mol Biol Rep, 37, 923-932.  
19805277 C.Dreyfus, D.Lemaire, S.Mari, D.Pignol, and P.Arnoux (2009).
Crystallographic snapshots of iterative substrate translocations during nicotianamine synthesis in Archaea.
  Proc Natl Acad Sci U S A, 106, 16180-16184.
PDB codes: 3fpe 3fpf 3fpg 3fph 3fpj
19244251 G.Minasov, S.Padavattan, L.Shuvalova, J.S.Brunzelle, D.J.Miller, A.Baslé, C.Massa, F.R.Collart, T.Schirmer, and W.F.Anderson (2009).
Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains.
  J Biol Chem, 284, 13174-13184.
PDB codes: 2bas 2w27
19196710 J.Lee, V.Sperandio, D.E.Frantz, J.Longgood, A.Camilli, M.A.Phillips, and A.J.Michael (2009).
An alternative polyamine biosynthetic pathway is widespread in bacteria and essential for biofilm formation in Vibrio cholerae.
  J Biol Chem, 284, 9899-9907.  
19596901 M.Dorsett, B.Westlund, and T.Schedl (2009).
METT-10, a putative methyltransferase, inhibits germ cell proliferative fate in Caenorhabditis elegans.
  Genetics, 183, 233-247.  
18653732 E.G.Minguet, F.Vera-Sirera, A.Marina, J.Carbonell, and M.A.Blázquez (2008).
Evolutionary diversification in polyamine biosynthesis.
  Mol Biol Evol, 25, 2119-2128.  
17563834 F.E.Jenney, and M.W.Adams (2008).
The impact of extremophiles on structural genomics (and vice versa).
  Extremophiles, 12, 39-50.  
18367445 H.Wu, J.Min, H.Zeng, D.E.McCloskey, Y.Ikeguchi, P.Loppnau, A.J.Michael, A.E.Pegg, and A.N.Plotnikov (2008).
Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism.
  J Biol Chem, 283, 16135-16146.
PDB codes: 3c6k 3c6m
17916066 M.C.Taylor, H.Kaur, B.Blessington, J.M.Kelly, and S.R.Wilkinson (2008).
Validation of spermidine synthase as a drug target in African trypanosomes.
  Biochem J, 409, 563-569.  
  19704464 M.Rodríguez-Kessler, and J.F.Jiménez-Bremont (2008).
Zmspds2 maize gene: Coding a spermine synthase?
  Plant Signal Behav, 3, 551-553.  
18186482 M.Roovers, Y.Oudjama, K.H.Kaminska, E.Purta, J.Caillet, L.Droogmans, and J.M.Bujnicki (2008).
Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.
  Proteins, 71, 2076-2085.  
18320213 R.C.Efrose, E.Flemetakis, L.Sfichi, C.Stedel, E.D.Kouri, M.K.Udvardi, K.Kotzabasis, and P.Katinakis (2008).
Characterization of spermidine and spermine synthases in Lotus japonicus: induction and spatial organization of polyamine biosynthesis in nitrogen fixing nodules.
  Planta, 228, 37-49.  
17932934 S.Wong, and M.P.Jacobson (2008).
Conformational selection in silico: loop latching motions and ligand binding in enzymes.
  Proteins, 71, 153-164.  
18484748 Y.Peng, Q.Feng, D.Wilk, A.A.Adjei, O.E.Salavaggione, R.M.Weinshilboum, and V.C.Yee (2008).
Structural basis of substrate recognition in thiopurine s-methyltransferase.
  Biochemistry, 47, 6216-6225.
PDB codes: 3bgd 3bgi
17586769 D.J.Miller, L.Shuvalova, E.Evdokimova, A.Savchenko, A.F.Yakunin, and W.F.Anderson (2007).
Structural and biochemical characterization of a novel Mn2+-dependent phosphodiesterase encoded by the yfcE gene.
  Protein Sci, 16, 1338-1348.  
17545282 G.Cacciapuoti, M.Porcelli, M.A.Moretti, F.Sorrentino, L.Concilio, V.Zappia, Z.J.Liu, W.Tempel, F.Schubot, J.P.Rose, B.C.Wang, P.S.Brereton, F.E.Jenney, and M.W.Adams (2007).
The first agmatine/cadaverine aminopropyl transferase: biochemical and structural characterization of an enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon Pyrococcus furiosus.
  J Bacteriol, 189, 6057-6067.  
17221359 M.Teuber, M.E.Azemi, F.Namjoyan, A.C.Meier, A.Wodak, W.Brandt, and B.Dräger (2007).
Putrescine N-methyltransferases--a structure-function analysis.
  Plant Mol Biol, 63, 787-801.  
17357156 P.K.Lu, J.Y.Tsai, H.Y.Chien, H.Huang, C.H.Chu, and Y.J.Sun (2007).
Crystal structure of Helicobacter pylori spermidine synthase: a Rossmann-like fold with a distinct active site.
  Proteins, 67, 743-754.
PDB codes: 2cmg 2cmh
16880714 K.Samejima (2006).
[Regulation of polyamine and cancer]
  Yakugaku Zasshi, 126, 529-542.  
16088399 O.Stenzel, M.Teuber, and B.Dräger (2006).
Putrescine N-methyltransferase in Solanum tuberosum L., a calystegine-forming plant.
  Planta, 223, 200-212.  
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
16364195 M.A.Medina, F.Correa-Fiz, C.Rodríguez-Caso, and F.Sánchez-Jiménez (2005).
A comprehensive view of polyamine and histamine metabolism to the light of new technologies.
  J Cell Mol Med, 9, 854-864.  
15609338 M.E.Cuff, D.J.Miller, S.Korolev, X.Xu, W.F.Anderson, A.Edwards, A.Joachimiak, and A.Savchenko (2005).
Crystal structure of a predicted precorrin-8x methylmutase from Thermoplasma acidophilum.
  Proteins, 58, 751-754.
PDB code: 1ou0
15983049 M.Ohnuma, Y.Terui, M.Tamakoshi, H.Mitome, M.Niitsu, K.Samejima, E.Kawashima, and T.Oshima (2005).
N1-aminopropylagmatine, a new polyamine produced as a key intermediate in polyamine biosynthesis of an extreme thermophile, Thermus thermophilus.
  J Biol Chem, 280, 30073-30082.  
16225687 P.Z.Kozbial, and A.R.Mushegian (2005).
Natural history of S-adenosylmethionine-binding proteins.
  BMC Struct Biol, 5, 19.  
15273252 A.Jansson, H.Koskiniemi, P.Mäntsälä, J.Niemi, and G.Schneider (2004).
Crystal structure of a ternary complex of DnrK, a methyltransferase in daunorubicin biosynthesis, with bound products.
  J Biol Chem, 279, 41149-41156.
PDB codes: 1tw2 1tw3
15340214 H.Goda, T.Watanabe, N.Takeda, M.Kobayashi, M.Wada, H.Hosoda, A.Shirahata, and K.Samejima (2004).
Mammalian spermidine synthase--identification of cysteine residues and investigation of the putrescine binding site--.
  Biol Pharm Bull, 27, 1327-1332.  
15502329 P.K.Lu, S.Y.Chien, J.Y.Tsai, C.T.Fong, M.J.Lee, H.Huang, and Y.J.Sun (2004).
Crystallization and preliminary X-ray diffraction analysis of spermidine synthase from Helicobacter pylori.
  Acta Crystallogr D Biol Crystallogr, 60, 2067-2069.  
15459188 X.Wang, Y.Ikeguchi, D.E.McCloskey, P.Nelson, and A.E.Pegg (2004).
Spermine synthesis is required for normal viability, growth, and fertility in the mouse.
  J Biol Chem, 279, 51370-51375.  
12954781 J.Osipiuk, M.A.Walsh, and A.Joachimiak (2003).
Crystal structure of MboIIA methyltransferase.
  Nucleic Acids Res, 31, 5440-5448.
PDB code: 1g60
12429089 J.P.Keller, P.M.Smith, J.Benach, D.Christendat, G.T.deTitta, and J.F.Hunt (2002).
The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase.
  Structure, 10, 1475-1487.
PDB codes: 1f38 1kxz 1l3b 1l3c 1l3i
11877432 R.G.Zhang, Y.Kim, T.Skarina, S.Beasley, R.Laskowski, C.Arrowsmith, A.Edwards, A.Joachimiak, and A.Savchenko (2002).
Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.
  J Biol Chem, 277, 19183-19190.
PDB code: 1mkm
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.