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(-) Description

Title :  THE STRUCTURE OF (3R)-HYDROXYACYL-ACP DEHYDRATASE (FABZ)
 
Authors :  M. S. Kimber, F. Martin, Y. Lu, S. Houston, M. Vedadi, A. Dharamsi, K. M. Fiebig, M. Schmid, C. O. Rock
Date :  16 Jul 04  (Deposition) - 28 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Dehydratase; Fatty Acid Biosynthesis; Hot Dog Fold, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Kimber, F. Martin, Y. Lu, S. Houston, M. Vedadi, A. Dharamsi, K. M. Fiebig, M. Schmid, C. O. Rock
The Structure Of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Pseudomonas Aeruginosa
J. Biol. Chem. V. 279 52593 2004
PubMed-ID: 15371447  |  Reference-DOI: 10.1074/JBC.M408105200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - (3R)-HYDROXYMYRISTOYL-[ACYL CARRIER PROTEIN] DEHYDRATASE
    Chains: A, B, C, D, E, F
    EC Number: 4.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)-GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FABZ
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: (3R)-HYDROXYMYRISTOYL ACP DEHYDRASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 35)

Asymmetric/Biological Unit (2, 35)
No.NameCountTypeFull Name
1MSE30Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG D:34 , HOH D:525BINDING SITE FOR RESIDUE SO4 D 500
2AC2SOFTWARELYS B:117 , ARG B:118 , SER B:119BINDING SITE FOR RESIDUE SO4 D 501
3AC3SOFTWARELYS B:117 , ARG B:118 , GLY D:84 , LYS D:145BINDING SITE FOR RESIDUE SO4 D 502
4AC4SOFTWAREARG D:118 , SER D:119 , ARG D:144BINDING SITE FOR RESIDUE SO4 D 503
5AC5SOFTWAREASP B:83 , LYS B:145 , LYS D:117 , ARG D:118BINDING SITE FOR RESIDUE SO4 D 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U1Z)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Tyr A:15 -Pro A:16
2His A:49 -Phe A:50
3Tyr B:15 -Pro B:16
4His B:49 -Phe B:50
5Tyr C:15 -Pro C:16
6His C:49 -Phe C:50
7Tyr D:15 -Pro D:16
8His D:49 -Phe D:50
9Tyr E:15 -Pro E:16
10His E:49 -Phe E:50
11Tyr F:15 -Pro F:16
12His F:49 -Phe F:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U1Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U1Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1U1Z)

(-) 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:142
 aligned with FABZ_PSEAE | Q9HXY7 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
           FABZ_PSEAE     1 MMDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPIMPGVLIIEAMAQAAGILGFKMLDVKPADGTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERK 145
               SCOP domains d1u1za_ A: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                               SCOP domains
               CATH domains --1u1zA00 A:3-145  [code=3.10.129.10, no name defined]                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.............eeeeee....eeeeeee......hhhhh.......hhhhhhhhhhhhhhhhhhhhhh...---.eeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u1z A   1 mmDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPImPGVLIIEAmAQAAGILGFKmLDVKP---TLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERK 145
                            ||      10        20        30        40        50     |  60    |   70     |  80|   |   90       100       110       120       130       140     
                            ||                                                    56-MSE   65-MSE     76-MSE1  85                                                            
                            1-MSE                                                                                                                                            
                             2-MSE                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with FABZ_PSEAE | Q9HXY7 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           FABZ_PSEAE     1 MMDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPIMPGVLIIEAMAQAAGILGFKMLDVKPADGTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKL 146
               SCOP domains d1u1zb_ B: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                SCOP domains
               CATH domains --1u1zB00 B:3-146  [code=3.10.129.10, no name defined]                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..........eeeeee....eeeeeee......hhhhh.......hhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u1z B   1 mmDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPImPGVLIIEAmAQAAGILGFKmLDVKPADGTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKL 146
                            ||      10        20        30        40        50     |  60    |   70     |  80        90       100       110       120       130       140      
                            1-MSE                                                 56-MSE   65-MSE     76-MSE                                                                  
                             2-MSE                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:146
 aligned with FABZ_PSEAE | Q9HXY7 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:148
                                                                                                                                                                           146  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     |  
           FABZ_PSEAE     1 MMDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPIMPGVLIIEAMAQAAGILGFKMLDVKPADGTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKL--   -
               SCOP domains d1u1zc_ C: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                  SCOP domains
               CATH domains --1u1zC00 C:3-148  [code=3.10.129.10, no name defined]                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..........eeeeee....eeeeeee......hhhhh.......hhhhhhhhhhhhhhhhhhhhh...--....eeeeeeeeeee........eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u1z C   1 mmDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPImPGVLIIEAmAQAAGILGFKmLDVK--DGTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKLGS 148
                            ||      10        20        30        40        50     |  60    |   70     |  80  |     90       100       110       120       130       140        
                            1-MSE                                                 56-MSE   65-MSE     76-MSE 83                                                                 
                             2-MSE                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:144
 aligned with FABZ_PSEAE | Q9HXY7 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           FABZ_PSEAE     1 MMDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPIMPGVLIIEAMAQAAGILGFKMLDVKPADGTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKL 146
               SCOP domains d1u1zd_ D: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                SCOP domains
               CATH domains --1u1zD00 D:3-146  [code=3.10.129.10, no name defined]                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..........eeeeee....eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....--.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u1z D   1 mmDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPImPGVLIIEAmAQAAGILGFKmLDVKP--GTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKL 146
                            ||      10        20        30        40        50     |  60    |   70     |  80|  |    90       100       110       120       130       140      
                            1-MSE                                                 56-MSE   65-MSE     76-MSE1 84                                                              
                             2-MSE                                                                                                                                            


Chain E from PDB  Type:PROTEIN  Length:145
 aligned with FABZ_PSEAE | Q9HXY7 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           FABZ_PSEAE     1 MMDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPIMPGVLIIEAMAQAAGILGFKMLDVKPADGTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKL 146
               SCOP domains d1u1ze_ E: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                SCOP domains
               CATH domains --1u1zE00 E:3-146  [code=3.10.129.10, no name defined]                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..........eeeeee....eeeeeee......hhhhh.......hhhhhhhhhhhhhhhhhhhhh.....-.eeeeeeeeeeeee........eeeeeeee......eeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u1z E   1 mmDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPImPGVLIIEAmAQAAGILGFKmLDVKPA-GTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKL 146
                            ||      10        20        30        40        50     |  60    |   70     |  80 | |    90       100       110       120       130       140      
                            1-MSE                                                 56-MSE   65-MSE     76-MSE82 |                                                              
                             2-MSE                                                                            84                                                              


Chain F from PDB  Type:PROTEIN  Length:146
 aligned with FABZ_PSEAE | Q9HXY7 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      
           FABZ_PSEAE     1 MMDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPIMPGVLIIEAMAQAAGILGFKMLDVKPADGTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKL 146
               SCOP domains d1u1zf_ F: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                SCOP domains
               CATH domains --1u1zF00 F:3-146  [code=3.10.129.10, no name defined]                                                                                             CATH domains
           Pfam domains (1) ----------FabA-1u1zF01 F:11-138                                                                                                           -------- Pfam domains (1)
           Pfam domains (2) ----------FabA-1u1zF02 F:11-138                                                                                                           -------- Pfam domains (2)
           Pfam domains (3) ----------FabA-1u1zF03 F:11-138                                                                                                           -------- Pfam domains (3)
           Pfam domains (4) ----------FabA-1u1zF04 F:11-138                                                                                                           -------- Pfam domains (4)
           Pfam domains (5) ----------FabA-1u1zF05 F:11-138                                                                                                           -------- Pfam domains (5)
           Pfam domains (6) ----------FabA-1u1zF06 F:11-138                                                                                                           -------- Pfam domains (6)
         Sec.struct. author ..hhhhhhhhh..........eeeeee....eeeeeee..................hhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u1z F   1 mmDINEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVSINEPFFNGHFPEHPImPGVLIIEAmAQAAGILGFKmLDVKPADGTLYYFVGSDKLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAERKL 146
                            ||      10        20        30        40        50     |  60    |   70     |  80        90       100       110       120       130       140      
                            1-MSE                                                 56-MSE   65-MSE     76-MSE                                                                  
                             2-MSE
   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, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: HotDog (52)
(-)
Family: FabA (8)
(-)
Pseudomonas aeruginosa (1)
1aFabA-1u1zF01F:11-138
1bFabA-1u1zF02F:11-138
1cFabA-1u1zF03F:11-138
1dFabA-1u1zF04F:11-138
1eFabA-1u1zF05F:11-138
1fFabA-1u1zF06F:11-138

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (FABZ_PSEAE | Q9HXY7)
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: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:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    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.
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:0009245    lipid A biosynthetic process    The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
    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.
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)

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(-) Related Entries Specified in the PDB File

1mka RELATED DEHYDRATASE/ISOMERASE
1mkb RELATED DEHYDRATASE/ISOMERASE