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PDBsum entry 1e5m
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Condensing enzyme PDB id
1e5m

 

 

 

 

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Contents
Protein chain
411 a.a. *
Waters ×349
* Residue conservation analysis
PDB id:
1e5m
Name: Condensing enzyme
Title: Beta ketoacyl acyl carrier protein synthase ii (kasii) from synechocystis sp.
Structure: Beta ketoacyl acyl carrier protein synthase ii. Chain: a. Synonym: kas ii. Engineered: yes
Source: Synechocystis sp.. Organism_taxid: 1148. Strain: pcc6803. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: synechocystis sp. Pcc6803
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
1.54Å     R-factor:   0.175     R-free:   0.199
Authors: M.Moche,P.Edwards,K.Dehesh,Y.Lindqvist
Key ref:
M.Moche et al. (2001). The crystal structure of beta-ketoacyl-acyl carrier protein synthase II from Synechocystis sp. at 1.54 A resolution and its relationship to other condensing enzymes. J Mol Biol, 305, 491-503. PubMed id: 11152607 DOI: 10.1006/jmbi.2000.4272
Date:
27-Jul-00     Release date:   16-Jan-01    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P73283  (FABF_SYNY3) -  3-oxoacyl-[acyl-carrier-protein] synthase 2 from Synechocystis sp. (strain PCC 6803 / Kazusa)
Seq:
Struc: 		416 a.a.
411 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.179  - beta-ketoacyl-[acyl-carrier-protein] synthase Ii.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (9Z)-hexadecenoyl-[ACP] + malonyl-[ACP] + H+ = 3-oxo-(11Z)- octadecenoyl-[ACP] + holo-[ACP] + CO2
(9Z)-hexadecenoyl-[ACP]
 + malonyl-[ACP]
 + H(+)
 = 3-oxo-(11Z)- octadecenoyl-[ACP]
 + holo-[ACP]
 + CO2
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1006/jmbi.2000.4272 J Mol Biol 305:491-503 (2001)
PubMed id: 11152607  
 
 
The crystal structure of beta-ketoacyl-acyl carrier protein synthase II from Synechocystis sp. at 1.54 A resolution and its relationship to other condensing enzymes.
M.Moche, K.Dehesh, P.Edwards, Y.Lindqvist.
 
  ABSTRACT  
 
Condensing enzymes, catalyzing the formation of carbon-carbon bonds in several biosynthetic pathways, have lately been recognized as potential drug targets against cancer and tuberculosis, as crucial for combinatorial biosynthesis of antibiotics and related compounds, and as determinants of plant oil composition. beta-Ketoacyl-ACP synthases (KAS) are the condensing enzymes present in the fatty acid biosynthesis pathway and are able to elongate an acyl chain bound to either co-enzyme A (CoA) or acyl carrier protein (ACP) with a two-carbon unit derived from malonyl-ACP. Several isoforms of KAS with different substrate specificity are present in most species. We have determined the crystal structure of KAS II from Synechocystis sp. PCC 6803 to 1.54 A resolution giving a detailed description of the active site geometry. In order to analyze the structure-function relationships in this class of enzymes in more detail, we have compared all presently known three-dimensional structures of condensing enzymes from different pathways. The comparison reveals that these enzymes can be divided into three structural and functional classes. This classification can be related to variations in the catalytic mechanism and the set of residues in the catalytic site, e.g. due to differences in the nature of the second substrate providing the two-carbon elongation unit. The variation in the acyl-carrier (ACP or CoA) specificity might also be connected to this classification and residues involved in ACP binding in structure class 2 can be suggested based on the comparison. Finally, the two subunits in the dimer contribute differently to formation of the substrate binding-pocket in the three structural classes.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Scheme of the chemical steps occurring in the fatty acid elongation reaction catalyzed by b-ketoacyl-ACP synthase. 		Figure 2.
Figure 2. The structure of the subunit of KAS II from Synechocystis sp. Regions that are conserved in the structural alignment of all condensing enzymes with known structure are shown in magenta. The Figure was prepared using MOLSCRIPT[48] and Raster3D [49].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 305, 491-503) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18666307 A.S.Worthington, G.H.Hur, J.L.Meier, Q.Cheng, B.S.Moore, and M.D.Burkart (2008).
Probing the compatibility of type II ketosynthase-carrier protein partners.
  Chembiochem, 9, 2096-2103.  
  18453702 B.Bagautdinov, Y.Ukita, M.Miyano, and N.Kunishima (2008).
Structure of 3-oxoacyl-(acyl-carrier protein) synthase II from Thermus thermophilus HB8.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 358-366.
PDB code: 1j3n
18219113 G.Parthasarathy, R.Cummings, J.W.Becker, and S.M.Soisson (2008).
Surface-entropy reduction approaches to manipulate crystal forms of beta-ketoacyl acyl carrier protein synthase II from Streptococcus pneumoniae.
  Acta Crystallogr D Biol Crystallogr, 64, 141-148.
PDB code: 2rjt
17242430 C.E.Christensen, B.B.Kragelund, P.von Wettstein-Knowles, and A.Henriksen (2007).
Structure of the human beta-ketoacyl [ACP] synthase from the mitochondrial type II fatty acid synthase.
  Protein Sci, 16, 261-272.
PDB codes: 2iwy 2iwz 2ix4
17268612 C.Hertweck, A.Luzhetskyy, Y.Rebets, and A.Bechthold (2007).
Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork.
  Nat Prod Rep, 24, 162-190.  
17174327 S.Sridharan, L.Wang, A.K.Brown, L.G.Dover, L.Kremer, G.S.Besra, and J.C.Sacchettini (2007).
X-ray crystal structure of Mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase II (mtKasB).
  J Mol Biol, 366, 469-480.
PDB code: 2gp6
16356722 A.M.Haapalainen, G.Meriläinen, and R.K.Wierenga (2006).
The thiolase superfamily: condensing enzymes with diverse reaction specificities.
  Trends Biochem Sci, 31, 64-71.  
16441657 P.von Wettstein-Knowles, J.G.Olsen, K.A.McGuire, and A.Henriksen (2006).
Fatty acid synthesis. Role of active site histidines and lysine in Cys-His-His-type beta-ketoacyl-acyl carrier protein synthases.
  FEBS J, 273, 695-710.
PDB codes: 1h4f 2buh 2bui 2byw 2byx 2byy 2byz 2bz3 2bz4
16618705 Y.M.Zhang, J.Hurlbert, S.W.White, and C.O.Rock (2006).
Roles of the active site water, histidine 303, and phenylalanine 396 in the catalytic mechanism of the elongation condensing enzyme of Streptococcus pneumoniae.
  J Biol Chem, 281, 17390-17399.
PDB code: 2alm
15668256 L.Zhang, A.K.Joshi, J.Hofmann, E.Schweizer, and S.Smith (2005).
Cloning, expression, and characterization of the human mitochondrial beta-ketoacyl synthase. Complementation of the yeast CEM1 knock-out strain.
  J Biol Chem, 280, 12422-12429.  
15952903 S.W.White, J.Zheng, Y.M.Zhang, and Rock (2005).
The structural biology of type II fatty acid biosynthesis.
  Annu Rev Biochem, 74, 791-831.  
15194690 H.Wang, and J.E.Cronan (2004).
Functional replacement of the FabA and FabB proteins of Escherichia coli fatty acid synthesis by Enterococcus faecalis FabZ and FabF homologues.
  J Biol Chem, 279, 34489-34495.  
15286723 R.Sankaranarayanan, P.Saxena, U.B.Marathe, R.S.Gokhale, V.M.Shanmugam, and R.Rukmini (2004).
A novel tunnel in mycobacterial type III polyketide synthase reveals the structural basis for generating diverse metabolites.
  Nat Struct Mol Biol, 11, 894-900.
PDB codes: 1ted 1tee
15052334 Y.J.Lu, Y.M.Zhang, and C.O.Rock (2004).
Product diversity and regulation of type II fatty acid synthases.
  Biochem Cell Biol, 82, 145-155.  
12837788 A.C.Price, C.O.Rock, and S.W.White (2003).
The 1.3-Angstrom-resolution crystal structure of beta-ketoacyl-acyl carrier protein synthase II from Streptococcus pneumoniae.
  J Bacteriol, 185, 4136-4143.
PDB codes: 1ox0 1oxh
12897013 H.Wang, and J.E.Cronan (2003).
Haemophilus influenzae Rd lacks a stringently conserved fatty acid biosynthetic enzyme and thermal control of membrane lipid composition.
  J Bacteriol, 185, 4930-4937.  
12866053 J.H.Dawe, C.T.Porter, J.M.Thornton, and A.B.Tabor (2003).
A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes.
  Proteins, 52, 427-435.  
12941968 P.Saxena, G.Yadav, D.Mohanty, and R.S.Gokhale (2003).
A new family of type III polyketide synthases in Mycobacterium tuberculosis.
  J Biol Chem, 278, 44780-44790.  
12689621 S.Smith, A.Witkowski, and A.K.Joshi (2003).
Structural and functional organization of the animal fatty acid synthase.
  Prog Lipid Res, 42, 289-317.  
12429097 H.Pan, S.Tsai, E.S.Meadows, L.J.Miercke, A.T.Keatinge-Clay, J.O'Connell, C.Khosla, and R.M.Stroud (2002).
Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway.
  Structure, 10, 1559-1568.
PDB code: 1mzj
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 code is shown on the right.

 

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