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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH 3-(PENTYLTHIO)-4H-1,2,4-TRIAZOLE
 
Authors :  L. Moynie, S. A. Mcmahon, F. G. Duthie, J. H. Naismith
Date :  01 Jul 12  (Deposition) - 28 Nov 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E  (2x)
Keywords :  Lyase, Fatty Acid Biosynthesis, Bacterial Virulence, Drug Discovery (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Moynie, S. M. Leckie, S. A. Mcmahon, F. G. Duthie, A. Koehnke, J. W. Taylor, M. S. Alphey, R. Brenk, A. D. Smith, J. H. Naismith
Structural Insights Into The Mechanism And Inhibition Of The Beta-Hydroxydecanoyl-Acyl Carrier Protein Dehydratase From Pseudomonasaeruginosa.
J. Mol. Biol. V. 425 365 2013
PubMed-ID: 23174186  |  Reference-DOI: 10.1016/J.JMB.2012.11.017

(-) Compounds

Molecule 1 - 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
    ChainsA, B, C, D, E
    EC Number4.2.1.60
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantTUNER
    Expression System VectorPDEST14
    Expression System Vector TypePLASMID
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287
    StrainPA01
    SynonymBETA-HYDROXYDECANOYL THIOESTER DEHYDRASE

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)AB   
Biological Unit 2 (1x)  CD 
Biological Unit 3 (2x)    E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1C9H5Ligand/Ion5-(PENTYLSULFANYL)-1H-1,2,4-TRIAZOLE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1C9H2Ligand/Ion5-(PENTYLSULFANYL)-1H-1,2,4-TRIAZOLE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1C9H2Ligand/Ion5-(PENTYLSULFANYL)-1H-1,2,4-TRIAZOLE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1C9H2Ligand/Ion5-(PENTYLSULFANYL)-1H-1,2,4-TRIAZOLE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:70 , GLY A:79 , GLY A:115 , HOH A:2002 , TRP B:87 , ALA B:105 , PHE B:171BINDING SITE FOR RESIDUE C9H A 501
2AC2SOFTWAREGLY A:103 , ARG A:104 , ALA A:105 , HOH A:2003 , MET B:77BINDING SITE FOR RESIDUE C9H B 501
3AC3SOFTWAREMET C:77 , GLY C:79 , ALA D:105 , PHE D:171BINDING SITE FOR RESIDUE C9H C 501
4AC4SOFTWAREASP C:84 , TRP C:87 , ALA C:105 , HIS D:70 , MET D:77 , GLY D:79 , TYR D:155BINDING SITE FOR RESIDUE C9H D 501
5AC5SOFTWAREHIS E:70 , MET E:77 , GLY E:79 , ALA E:105 , GLY E:115 , TYR E:155BINDING SITE FOR RESIDUE C9H E 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B0C)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Pro A:31 -Asn A:32
2His A:70 -Phe A:71
3Pro B:31 -Asn B:32
4His B:70 -Phe B:71
5Pro C:31 -Asn C:32
6His C:70 -Phe C:71
7Pro D:31 -Asn D:32
8His D:70 -Phe D:71
9Pro E:31 -Asn E:32
10His E:70 -Phe E:71

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B0C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B0C)

(-) Exons   (0, 0)

(no "Exon" information available for 4B0C)

(-) 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:168
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
           FABA_PSEAE     2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
               SCOP domains d4b0ca_ A: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh....................eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..............eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee...--. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0c A   2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTST--F 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      |171
                                                                                                                                                                                                168  |
                                                                                                                                                                                                   171

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
           FABA_PSEAE     2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
               SCOP domains d4b0cb_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh..............................................hhhhhhh.......hhhhhhhhhhhhhhhhhhhh.............eee......................................eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0c B   2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain C from PDB  Type:PROTEIN  Length:166
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           FABA_PSEAE     2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTD 169
               SCOP domains d4b0cc_ C: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhh....................eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..............eeeeeeeeeeee.--.eeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4b0c C   2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTIN--LVLAIADGTVSVDGREIYSAEGLRVGLFTSTD 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   |  |141       151       161        
                                                                                                                                                               135  |                               
                                                                                                                                                                  138                               

Chain D from PDB  Type:PROTEIN  Length:169
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
           FABA_PSEAE     1 MTKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
               SCOP domains d4b0cd_ D: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..............................................hhhhhhh.......hhhhhhhhhhhhhhhhhhhh.............eee......................--..............eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0c D   1 MTKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTIN--LVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    |  140       150       160       170 
                                                                                                                                                                135  |                                 
                                                                                                                                                                   138                                 

Chain E from PDB  Type:PROTEIN  Length:169
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:169
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162         
           FABA_PSEAE     3 KQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
               SCOP domains d4b0ce_ E: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....................eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeee...eee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0c E   3 KQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162         

   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, 5)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B0C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B0C)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (FABA_PSEAE | O33877)
molecular function
    GO:0019171    3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity    Catalysis of the reaction: a (3R)-3-hydroxyacyl-[acyl-carrier protein] = H2O + a trans-delta2-enoyl-acyl-[acyl-carrier protein].
    GO:0008693    3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity    Catalysis of the reaction: (3R)-3-hydroxydecanoyl-[acyl-carrier protein] = 2,3-decenoyl-[acyl-carrier protein] or 3,4-decenoyl-[acyl-carrier protein] + H2O.
    GO:0047451    3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity    Catalysis of the reaction: (3R)-3-hydroxyoctanoyl-[acyl-carrier protein] = H2O + 2-octenoyl-[acyl-carrier protein].
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0034017    trans-2-decenoyl-acyl-carrier-protein isomerase activity    Catalysis of the reaction: trans-dec-2-enoyl-[acyl-carrier protein] = cis-dec-3-enoyl-[acyl-carrier protein].
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:0006636    unsaturated fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of an unsaturated fatty acid, any fatty acid containing one or more double bonds between carbon atoms.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FABA_PSEAE | O338774b0b 4b0i 4b0j 4b8u 4cl6 4fq9

(-) Related Entries Specified in the PDB File

4b0b CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH 3-(PYRIDIN-2-YLOXY)ANILINE
4b0i CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) MUTANT (H70N) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH 3-HYDROXYDECANOYL-N-ACETYL CYSTEAMINE
4b8u CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH N-ISOBUTYL-2-(5-(2-THIENYL)-1,2- OXAZOL-3-YL-)METHOXY)ACETAMIDE
4fq9 CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) FROM PSEUDOMONAS AERUGINOSA