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(-) Description

Title :  METHANETHIOL-CYS 112 INHIBITION COMPLEX OF E. COLI KETOACYL SYNTHASE III (FABH) AND COENZYME A (HIGH CONCENTRATION (1.7MM) SOAK)
 
Authors :  M. M. Alhamadsheh, F. Musayev, A. A. Komissarov, S. Sachdeva, H. T. Wrig N. Scarsdale, G. Florova, K. A. Reynolds
Date :  24 Feb 07  (Deposition) - 12 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fatty Acid Biosynthesis, Alkyl-Coa-Disulfide, Mechanism-Based Inhibitor, E. Coli, Half Sites Occupancy, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Alhamadsheh, F. Musayev, A. A. Komissarov, S. Sachdeva, H. T. Wright, N. Scarsdale, G. Florova, K. A. Reynolds
Alkyl-Coa Disulfides As Inhibitors And Mechanistic Probes For Fabh Enzymes
Chem. Biol. V. 14 513 2007
PubMed-ID: 17524982  |  Reference-DOI: 10.1016/J.CHEMBIOL.2007.03.013

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3
    Chains: A, B
    EC Number: 2.3.1.41
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3 PLYSE)/PLH14
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FABH
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 3-OXOACYL- [ACYL-CARRIER-PROTEIN] SYNTHASE III, BETA- KETOACYL-ACP SYNTHASE III, KAS III, ECFABH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2MEE2Ligand/IonMETHANETHIOL
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:261 , MET B:262 , HOH B:995BINDING SITE FOR RESIDUE SO4 B 501
2AC2SOFTWARELEU A:179 , HOH A:1120 , PRO B:104 , HOH B:1031BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWARETHR A:28 , TRP A:32 , ARG A:36 , ARG A:151 , MET A:207 , GLY A:209 , ASN A:210 , ALA A:246 , ARG A:249 , ASN A:274 , PHE A:304 , MEE A:963 , ARG B:40BINDING SITE FOR RESIDUE COA A 962
4AC4SOFTWARECYS A:112 , LEU A:142 , GLY A:306 , COA A:962 , PHE B:87BINDING SITE FOR RESIDUE MEE A 963
5AC5SOFTWAREILE B:73 , GLN B:95 , CYS B:103BINDING SITE FOR RESIDUE MEE B 964

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EFT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:87 -Pro A:88
2Phe B:87 -Pro B:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EFT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EFT)

(-) Exons   (0, 0)

(no "Exon" information available for 2EFT)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:317
 aligned with FABH_ECOLI | P0A6R0 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:317
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       
           FABH_ECOLI     1 MYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFEAATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDVAAACAGFTYALSVADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDGAGAAVLAASEEPGIISTHLHADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQLDWLVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASVPCALDEAVRDGRIKPGQLVLLEAFGGGFTWGSALVRF 317
               SCOP domains d2efta1 A:1-174 Ketoacyl-ACP synthase III (FabH)                                                                                                                              d2efta2 A:175-317 Ketoacyl-ACP synthase III (FabH)                                                                                              SCOP domains
               CATH domains 2eftA01 A:1-170  [code=3.40.47.10, no name defined]                                                                                                                       2eftA02 A:171-317  [code=3.40.47.10, no name defined]                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee...eeeehhhhhhhh..hhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhh.hhh.eeeeeee.....eee.hhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhh...hhhhhh....eeeeeeeeee....eeeeeeee.hhhhh.eeee.............eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eft A   1 MYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFEAATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDVAAACAGFTYALSVADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDGAGAAVLAASEEPGIISTHLHADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQLDWLVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASVPCALDEAVRDGRIKPGQLVLLEAFGGGFTWGSALVRF 317
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       


Chain B from PDB  Type:PROTEIN  Length:317
 aligned with FABH_ECOLI | P0A6R0 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:317
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       
           FABH_ECOLI     1 MYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFEAATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDVAAACAGFTYALSVADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDGAGAAVLAASEEPGIISTHLHADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQLDWLVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASVPCALDEAVRDGRIKPGQLVLLEAFGGGFTWGSALVRF 317
               SCOP domains d2eftb1 B:1-174 Ketoacyl-ACP synthase III (FabH)                                                                                                                              d2eftb2 B:175-317 Ketoacyl-ACP synthase III (FabH)                                                                                              SCOP domains
               CATH domains 2eftB01 B:1-170  [code=3.40.47.10, no name defined]                                                                                                                       2eftB02 B:171-317  [code=3.40.47.10, no name defined]                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee...eeeehhhhhhhh..hhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.....eee.hhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhh...hhhhhh....eeeeeeeeee....eeeeeeee.hhhhh.eeee.............eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhh.hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eft B   1 MYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFEAATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDVAAACAGFTYALSVADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDGAGAAVLAASEEPGIISTHLHADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQLDWLVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASVPCALDEAVRDGRIKPGQLVLLEAFGGGFTWGSALVRF 317
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EFT)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FABH_ECOLI | P0A6R0)
molecular function
    GO:0004315    3-oxoacyl-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein].
    GO:0033818    beta-ketoacyl-acyl-carrier-protein synthase III activity    Catalysis of the reaction: acetyl-CoA + malonyl-[acyl-carrier protein] = acetoacyl-[acyl-carrier protein] + CoA + CO2.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FABH_ECOLI | P0A6R0: 1ebl 1hn9 1hnd 1hnh 1hnj 1hnk 1mzs 2gyo 3il9 4z8d 5bnm 5bnr 5bns

(-) Related Entries Specified in the PDB File

1ebl THE 1.8 A CRYSTAL STRUCTURE AND ACTIVE SITE ARCHITECTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE III (FABH) FROM ESHERICHIA COLI
1hnd CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III-COA COMPLEX
2gyo METHANETHIOL-CYS 112 INHIBITION COMPLEX OF E. COLI KETOACYL SYNTHASE III (FABH) AND COENZYME A