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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-(ACYL CARRIER PROTEIN) DEHYDRATASE FROM YERSINIA PESTIS
 
Authors :  R. Zhang, N. Maltseva, K. Kwon, W. F. Anderson, A. Joachimiak, Center F Structural Genomics Of Infectious Diseases (Csgid)
Date :  30 Dec 10  (Deposition) - 12 Jan 11  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta Fold, Hotdog Fold, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, N. Maltseva, K. Kwon, W. F. Anderson, A. Joachimiak, Csgid
Crystal Structure Of 3-Hydroxydecanoyl-(Acyl Carrier Protein) Dehydratase From Yersinia Pestis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: FABA, YPTB1450
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: BETA-HYDROXYDECANOYL THIOESTER DEHYDRASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:116 , GLN A:117 , HOH A:218 , HOH A:249 , LEU B:107BINDING SITE FOR RESIDUE MES A 175
2AC2SOFTWAREARG A:105 , LEU A:107 , PHE A:166 , ASP A:168 , THR A:169 , HOH A:187 , PHE B:114 , GLY B:116 , GLN B:117BINDING SITE FOR RESIDUE MES A 173

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q62)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:71 -Phe A:72
2His B:71 -Phe B:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q62)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q62)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q62)

(-) 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:170
 aligned with FABA_YERPS | Q66CF3 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:172
                               1                                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167  
           FABA_YERPS     - ---MVDKRESYTKEDLEASGRGELFGAGGPPLPAGNMLMMDRIVKMIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVIMRKLIMGVADGEVLVDGKVIYTATDLKVGLFKDT 169
               SCOP domains d3q62a_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..eee.........eeeeeeeeeeee.--..eeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q62 A  -2 SNAMVDKRESYTKEDLEASGRGELFGAGGPPLPAGNMLMMDRIVKMIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVIM--LIMGVADGEVLVDGKVIYTATDLKVGLFKDT 169
                                     7        17        27        37        47        57        67        77        87        97       107       117       127        |- |     147       157       167  
                                                                                                                                                                    136  |                              
                                                                                                                                                                       139                              


Chain B from PDB  Type:PROTEIN  Length:171
 aligned with FABA_YERPS | Q66CF3 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:171
                              1                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168 
           FABA_YERPS     - --MVDKRESYTKEDLEASGRGELFGAGGPPLPAGNMLMMDRIVKMIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVIMRKLIMGVADGEVLVDGKVIYTATDLKVGLFKDT 169
               SCOP domains d3q62b_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------FabA-3q62B01 B:29-159                                                                                                              ---------- Pfam domains (1)
           Pfam domains (2) ------------------------------FabA-3q62B02 B:29-159                                                                                                              ---------- Pfam domains (2)
         Sec.struct. author ..........hhhhhhhhhh............hhhhh...eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..eee.........eeeeeeeeeeeee...eeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q62 B  -1 NAMVDKRESYTKEDLEASGRGELFGAGGPPLPAGNMLMMDRIVKMIEDGGSHNKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPDAKKVTYRINFKRVIMRKLIMGVADGEVLVDGKVIYTATDLKVGLFKDT 169
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q62)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HotDog (52)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FABA_YERPS | Q66CF3)
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.
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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  3q62
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