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(-) Description

Title :  CRYSTAL STRUCTURE OF (3R)-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABZ) FROM HELICOBACTER PYLORI IN COMPLEX WITH EMODIN
 
Authors :  L. Zhang, H. Zhang, W. Liu, Y. Guo, X. Shen, H. Jiang
Date :  02 Sep 08  (Deposition) - 21 Jul 09  (Release) - 21 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Fabz Complex, Emodin, Cytoplasm, Lipid A Biosynthesis, Lipid Synthesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Chen, L. Zhang, Y. Zhang, H. Zhang, J. Du, J. Ding, Y. Guo, H. Jiang, X. Shen
Emodin Targets The Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase From Helicobacter Pylori: Enzymatic Inhibition Assay With Crystal Structural And Thermodynamic Characterization
Bmc Microbiol. V. 9 91 2009
PubMed-ID: 19433000  |  Reference-DOI: 10.1186/1471-2180-9-91
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - (3R)-HYDROXYMYRISTOYL-ACYL CARRIER PROTEIN DEHYDRATASE
    ChainsA, B, C, D, E, F
    EC Number4.2.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainM15
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneFABZ
    Organism ScientificHELICOBACTER PYLORI
    Organism Taxid210
    StrainSS1

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1BEN7Ligand/IonBENZAMIDINE
2CL6Ligand/IonCHLORIDE ION
3EMO2Ligand/Ion3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:40 , GLU A:124 , VAL A:125 , THR E:138 , GLU E:148 , BEN E:161BINDING SITE FOR RESIDUE BEN A 160
02AC2SOFTWAREMET A:131 , MET A:154 , ILE A:155 , LEU F:86 , ASP F:90 , ILE F:93BINDING SITE FOR RESIDUE BEN A 161
03AC3SOFTWAREHIS A:58 , GLY A:67 , EMO A:163BINDING SITE FOR RESIDUE CL A 162
04AC4SOFTWAREPHE A:59 , PHE A:109 , ARG A:110 , ILE A:111 , PRO A:112 , CL A:162 , HOH A:165 , HOH A:226 , HOH A:257 , ILE B:98 , TYR B:100 , HOH B:243BINDING SITE FOR RESIDUE EMO A 163
05AC5SOFTWAREILE B:20 , LEU B:21 , HIS B:23 , PHE B:83 , LYS B:97 , ILE B:98 , VAL B:99BINDING SITE FOR RESIDUE BEN B 160
06AC6SOFTWARETRP B:87 , GLY B:88 , HOH B:240 , LEU E:86 , GLY E:130BINDING SITE FOR RESIDUE BEN B 161
07AC7SOFTWAREHOH A:175 , HIS B:58 , GLY B:67BINDING SITE FOR RESIDUE CL B 162
08AC8SOFTWAREGLY C:67 , HOH D:231BINDING SITE FOR RESIDUE CL C 160
09AC9SOFTWAREILE C:20 , LEU C:21 , PRO C:22 , HIS C:23 , ALA C:75 , GLN C:76 , GLY C:79 , PHE C:80 , PHE C:83 , LYS C:97 , ILE C:98 , VAL C:99 , PHE C:101 , ARG C:158 , HOH C:164 , HOH C:226 , HOH C:229 , PHE D:59BINDING SITE FOR RESIDUE EMO C 161
10BC1SOFTWAREALA C:38 , THR C:84 , SER C:85 , LEU C:86 , TRP C:87 , GLY C:88 , GLN D:40 , HOH D:212BINDING SITE FOR RESIDUE BEN D 160
11BC2SOFTWAREGLY D:67BINDING SITE FOR RESIDUE CL D 161
12BC3SOFTWARETHR A:138 , GLU A:148 , HOH A:222 , GLU E:124 , VAL E:125 , LEU E:126BINDING SITE FOR RESIDUE BEN E 160
13BC4SOFTWAREBEN A:160 , HOH A:222 , GLY E:136 , GLY E:137 , ALA E:149 , GLU E:150BINDING SITE FOR RESIDUE BEN E 161
14BC5SOFTWAREGLY E:67 , HOH F:244BINDING SITE FOR RESIDUE CL E 162
15BC6SOFTWAREHOH E:209 , HIS F:58 , GLY F:67BINDING SITE FOR RESIDUE CL F 160

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ED0)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Tyr A:25 -Pro A:26
2His A:58 -Phe A:59
3Tyr B:25 -Pro B:26
4His B:58 -Phe B:59
5Tyr C:25 -Pro C:26
6His C:58 -Phe C:59
7Tyr D:25 -Pro D:26
8His D:58 -Phe D:59
9Tyr E:25 -Pro E:26
10His E:58 -Phe E:59
11Tyr F:25 -Pro F:26
12His F:58 -Phe F:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ED0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ED0)

(-) Exons   (0, 0)

(no "Exon" information available for 3ED0)

(-) 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:152
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:152
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157  
         Q5G940_HELPX     8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
               SCOP domains d3ed0a_ A: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                      SCOP domains
               CATH domains 3ed0A00 A:8-159  [code=3.10.129.10, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhhh..........eeeeee...eeeeeee.....hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ed0 A   8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157  

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:150
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
         Q5G940_HELPX    10 SQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
               SCOP domains d3ed0b_ B: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                    SCOP domains
               CATH domains 3ed0B00 B:10-159  [code=3.10.129.10, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ed0 B  10 SQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159

Chain C from PDB  Type:PROTEIN  Length:150
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:150
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158
         Q5G940_HELPX     9 QSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAER 158
               SCOP domains d3ed0c_ C: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                    SCOP domains
               CATH domains 3ed0C00 C:9-158  [code=3.10.129.10, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ed0 C   9 QSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAER 158
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:152
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157  
         Q5G940_HELPX     8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
               SCOP domains d3ed0d_ D: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                      SCOP domains
               CATH domains 3ed0D00 D:8-159  [code=3.10.129.10, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ed0 D   8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157  

Chain E from PDB  Type:PROTEIN  Length:151
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:151
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
         Q5G940_HELPX     9 QSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
               SCOP domains d3ed0e_ E: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                     SCOP domains
               CATH domains 3ed0E00 E:9-159  [code=3.10.129.10, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ed0 E   9 QSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 

Chain F from PDB  Type:PROTEIN  Length:148
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:148
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         Q5G940_HELPX    11 QFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAER 158
               SCOP domains d3ed0f_ F: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                  SCOP domains
               CATH domains 3ed0F00 F:11-158  [code=3.10.129.10, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ed0 F  11 QFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAER 158
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150        

   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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ED0)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q5G940_HELPX | Q5G940)
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)

UniProtKB/Swiss-Prot
        Q5G940_HELPX | Q5G9402gll 2glm 2glp 2glv
UniProtKB/TrEMBL
        Q5G940_HELPX | Q5G9403b7j 3cf8 3cf9 3d04 3doy 3doz 3dp0 3dp1 3dp2 3dp3 4zjb

(-) Related Entries Specified in the PDB File

2gll