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(-) Description

Title :  STRUCTURE OF THE ENOYL-ACP REDUCTASE FABV FROM YERSINIA PESTIS WITH THE COFACTOR NADH (MR, CLEAVED HISTAG)
 
Authors :  M. W. Hirschbeck, J. Kuper, C. Kisker
Date :  13 Jul 11  (Deposition) - 18 Jan 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Fatty Acid Biosynthesis Ii, Short-Chain Dehydrogenase Reductase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Hirschbeck, J. Kuper, H. Lu, N. Liu, C. Neckles, S. Shah, S. Wagner C. A. Sotriffer, P. J. Tonge, C. Kisker
Structure Of The Yersinia Pestis Fabv Enoyl-Acp Reductase And Its Interaction With Two 2-Pyridone Inhibitors
Structure V. 20 89 2012
PubMed-ID: 22244758  |  Reference-DOI: 10.1016/J.STR.2011.07.019

(-) Compounds

Molecule 1 - PUTATIVE REDUCTASE YPO4104/Y4119/YP_4011
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: ENOYL-ACP REDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:48 , ALA A:49 , SER A:50 , THR A:51 , GLY A:52 , TYR A:53 , PHE A:73 , PHE A:74 , GLU A:75 , GLY A:110 , ASP A:111 , ALA A:112 , PHE A:113 , SER A:138 , LEU A:139 , ALA A:140 , SER A:141 , PHE A:223 , THR A:224 , TYR A:225 , LYS A:244 , LYS A:272 , ALA A:273 , VAL A:274 , SER A:276 , ALA A:278 , SER A:279 , NA A:1405 , HOH A:2105 , HOH A:2108 , HOH A:2192 , HOH A:2197 , HOH A:2199 , HOH A:2269 , HOH A:2304 , HOH A:2308 , HOH A:2419BINDING SITE FOR RESIDUE NAI A1400
2AC2SOFTWAREASP A:172 , GLU A:303 , SER A:311 , TYR A:334 , LYS A:335 , HOH A:2298 , HOH A:2420 , HOH A:2421BINDING SITE FOR RESIDUE GOL A1401
3AC3SOFTWAREASP A:111 , PHE A:113 , ARG A:143 , ARG A:144 , THR A:145 , HOH A:2201 , HOH A:2422BINDING SITE FOR RESIDUE GOL A1402
4AC4SOFTWAREGLU A:79 , GLU A:80 , LYS A:106 , ASP A:390 , ASN A:395 , ILE A:397BINDING SITE FOR RESIDUE GOL A1403
5AC5SOFTWAREPRO A:77 , TRP A:88 , ASP A:390 , LYS A:392 , HOH A:2412 , HOH A:2416 , HOH A:2423BINDING SITE FOR RESIDUE GOL A1404
6AC6SOFTWAREGLY A:48 , THR A:51 , GLY A:54 , SER A:138 , NAI A:1400BINDING SITE FOR RESIDUE NA A1405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZU3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZU3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZU3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZU3)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZU3)

(-) 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:405
 aligned with FABV_YERPE | Q8Z9U1 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:405
                                  1                                                                                                                                                                                                                                                                                                                                                                                                              
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394     
           FABV_YERPE     - ------MIIKPRVRGFICVTAHPTGCEANVKKQIDYVTTEGPIANGPKRVLVIGASTGYGLAARITAAFGCGADTLGVFFERPGEEGKPGTSGWYNSAAFHKFAAQKGLYAKSINGDAFSDEIKQLTIDAIKQDLGQVDQVIYSLASPRRTHPKTGEVFNSALKPIGNAVNLRGLDTDKEVIKESVLQPATQSEIDSTVAVMGGEDWQMWIDALLDAGVLAEGAQTTAFTYLGEKITHDIYWNGSIGAAKKDLDQKVLAIRESLAAHGGGDARVSVLKAVVTQASSAIPMMPLYLSLLFKVMKEKGTHEGCIEQVYSLYKDSLCGDSPHMDQEGRLRADYKELDPEVQNQVQQLWDQVTNDNIYQLTDFVGYKSEFLNLFGFGIDGVDYDADVNPDVKIPNLIQG 399
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh......ee..ee...hhhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeeee.....eee......eee.........eeeeeee....eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.............ee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....................eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zu3 A  -5 GSHMLEMIIKPRVRGFICVTAHPTGCEANVKKQIDYVTTEGPIANGPKRVLVIGASTGYGLAARITAAFGCGADTLGVFFERPGEEGKPGTSGWYNSAAFHKFAAQKGLYAKSINGDAFSDEIKQLTIDAIKQDLGQVDQVIYSLASPRRTHPKTGEVFNSALKPIGNAVNLRGLDTDKEVIKESVLQPATQSEIDSTVAVMGGEDWQMWIDALLDAGVLAEGAQTTAFTYLGEKITHDIYWNGSIGAAKKDLDQKVLAIRESLAAHGGGDARVSVLKAVVSQASSAIPMMPLYLSLLFKVMKEKGTHEGCIEQVYSLYKDSLCGDSPHMDQEGRLRADYKELDPEVQNQVQQLWDQVTNDNIYQLTDFVGYKSEFLNLFGFGIDGVDYDADVNPDVKIPNLIQG 399
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394
   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  (0, 0)

(no "SCOP Domain" information available for 3ZU3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZU3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZU3)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FABV_YERPE | Q8Z9U1)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0004318    enoyl-[acyl-carrier-protein] reductase (NADH) activity    Catalysis of the reaction: acyl-[acyl-carrier protein] + NAD+ = trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FABV_YERPE | Q8Z9U1: 3zu2 3zu4 3zu5 4bkq 5jai 5jam 5jaq

(-) Related Entries Specified in the PDB File

3zu2 STRUCTURE OF THE ENOYL-ACP REDUCTASE FABV FROM YERSINIA PESTIS WITH THE COFACTOR NADH (SIRAS)
3zu4 STRUCTURE OF THE ENOYL-ACP REDUCTASE FABV FROM YERSINIA PESTIS WITH THE COFACTOR NADH AND THE 2- PYRIDONE INHIBITOR PT172
3zu5 STRUCTURE OF THE ENOYL-ACP REDUCTASE FABV FROM YERSINIA PESTIS WITH THE COFACTOR NADH AND THE 2- PYRIDONE INHIBITOR PT173