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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III WITH BOUND DICHLOROBENZYLOXY-INDOLE-CARBOXYLIC ACID INHIBITOR
 
Authors :  R. A. Daines, I. Pendrak, K. Sham, G. S. Van Aller, A. K. Konstantinidis J. T. Lonsdale, C. A. Janson, X. Qui, M. Brandt, C. Silverman, M. S. Head
Date :  09 Oct 02  (Deposition) - 13 Nov 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Fabh, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. A. Daines, I. Pendrak, K. Sham, G. S. Van Aller, A. K. Konstantinidis, J. T. Lonsdale, C. A. Janson, X. Qiu, M. Brandt, S. S. Khandekar, C. Silverman, M. S. Head
First X-Ray Cocrystal Structure Of A Bacterial Fabh Condensing Enzyme And A Small Molecule Inhibitor Achieved Using Rational Design And Homology Modeling
J. Med. Chem. V. 46 5 2003
PubMed-ID: 12502353  |  Reference-DOI: 10.1021/JM025571B

(-) Compounds

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III
    ChainsA
    EC Number2.3.1.41
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymBETA-KETOACYL-ACP SYNTHASE III, KAS III

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
16691Ligand/Ion1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
16691Ligand/Ion1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
16692Ligand/Ion1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID
2OCS2Mod. Amino AcidCYSTEINESULFONIC ACID
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:16 , ASP A:21 , GLU A:171BINDING SITE FOR RESIDUE PO4 A 340
2AC2SOFTWARETRP A:32 , ARG A:36 , THR A:37 , PRO A:47 , OCS A:112 , ARG A:151 , GLY A:152 , LEU A:189 , MET A:207 , GLY A:209 , PHE A:213 , ALA A:216 , ALA A:246 , ASN A:247 , ILE A:250 , PHE A:304 , HOH A:519 , HOH A:528 , HOH A:546BINDING SITE FOR RESIDUE 669 A 350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MZS)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:87 -Pro A:88
2Pro A:172 -Gly A:173
3Gly A:307 -Phe A:308

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MZS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MZS)

(-) Exons   (0, 0)

(no "Exon" information available for 1MZS)

(-) Sequences/Alignments

Asymmetric 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 d1mzsa1 A:1-174 Ketoacyl-ACP synthase III (FabH)                                                                                                                              d1mzsa2 A:175-317 Ketoacyl-ACP synthase III (FabH)                                                                                              SCOP domains
               CATH domains 1mzsA01 A:1-170  [code=3.40.47.10, no name defined]                                                                                                                       1mzsA02 A:171-317  [code=3.40.47.10, no name defined]                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------ACP_syn_III-1mzsA01 A:106-183                                                 --------------------------------------------ACP_syn_III_C-1mzsA02 A:228-317                                                            Pfam domains
         Sec.struct. author .eeeeeeeeee....eeehhhhhh....hhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhh...hhhhhh....eeeeeeeeee....eeeeeeee.hhhhh.ee...............eehhhhhhhhhhhhhhhhhhhhhhh...hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mzs 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       
                                                                                                                                         112-OCS                                                                                                                                                                                                         

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Thiolase (72)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 | P0A6R01ebl 1hn9 1hnd 1hnh 1hnj 1hnk 2eft 2gyo 3il9 4z8d 5bnm 5bnr 5bns

(-) Related Entries Specified in the PDB File

1hn9 CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III
1hnd CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III-COA COMPLEX
1hnh CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III AND DEGRADED FORM OF ACETYL-COA
1hnj CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III AND MALONYL-COA