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(-) Description

Title :  THE CRYSTAL STRUCTURE AND REACTION MECHANISM OF E. COLI 2,4-DIENOYL COA REDUCTASE
 
Authors :  P. A. Hubbard, X. Liang, H. Schulz, J. J. Kim
Date :  20 Jun 03  (Deposition) - 30 Sep 03  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Iron-Sulfur, Tim Barrel, Flavodoxin, Flavin, Electron Transfer, Hydride Transfer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Hubbard, X. Liang, H. Schulz, J. J. Kim
The Crystal Structure And Reaction Mechanism Of Escherichia Coli 2, 4-Dienoyl-Coa Reductase
J. Biol. Chem. V. 278 37553 2003
PubMed-ID: 12840019  |  Reference-DOI: 10.1074/JBC.M304642200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2,4-DIENOYL-COA REDUCTASE
    Chains: A
    EC Number: 1.3.1.34
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PND-1
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FADH
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 2,4-DIENOYL COENZYME A REDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
4MDE1Ligand/Ion5-MERCAPTOETHANOL-2-DECENOYL-COENZYME A
5NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
6SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:406BINDING SITE FOR RESIDUE CL A 705
2AC2SOFTWAREASN A:75BINDING SITE FOR RESIDUE CL A 706
3AC3SOFTWAREHIS A:361BINDING SITE FOR RESIDUE CL A 707
4AC4SOFTWAREARG A:311 , CYS A:334 , ILE A:335 , CYS A:337 , ASN A:338 , ALA A:340 , CYS A:341 , CYS A:353 , LEU A:354BINDING SITE FOR RESIDUE SF4 A 700
5AC5SOFTWAREGLN A:339 , LEU A:354 , GLY A:380 , GLY A:382 , PRO A:383 , ALA A:384 , ASP A:403 , ALA A:404 , HIS A:405 , GLY A:410 , GLN A:411 , PHE A:412 , ILE A:414 , ALA A:415 , LYS A:421 , PHE A:424 , HIS A:446 , VAL A:448 , ALA A:462 , SER A:463 , GLY A:464 , LEU A:487 , ASP A:508 , ASN A:629 , GLY A:647 , GLY A:648 , LEU A:655 , ASP A:656 , ALA A:657 , NAP A:703 , HOH A:787 , HOH A:961 , HOH A:1026BINDING SITE FOR RESIDUE FAD A 701
6AC6SOFTWARESER A:24 , MET A:25 , HIS A:26 , GLY A:58 , GLN A:100 , MET A:161 , ARG A:214 , THR A:286 , ASN A:287 , ARG A:288 , MET A:309 , ALA A:310 , ARG A:311 , CYS A:341 , MDE A:704 , HOH A:708 , HOH A:709 , HOH A:949 , HOH A:956BINDING SITE FOR RESIDUE FMN A 702
7AC7SOFTWAREGLN A:339 , ARG A:468 , GLY A:504 , ILE A:505 , GLN A:561 , ARG A:562 , LYS A:563 , LEU A:571 , TYR A:596 , CYS A:623 , ALA A:624 , GLY A:625 , MET A:653 , GLU A:654 , LEU A:655 , ASP A:656 , FAD A:701 , HOH A:721 , HOH A:777 , HOH A:918 , HOH A:967 , HOH A:968 , HOH A:974 , HOH A:975 , HOH A:985BINDING SITE FOR RESIDUE NAP A 703
8AC8SOFTWAREHIS A:26 , LEU A:102 , THR A:104 , PRO A:122 , GLU A:164 , TYR A:166 , ARG A:175 , HIS A:252 , GLU A:253 , ARG A:255 , THR A:258 , ILE A:259 , PHE A:346 , LYS A:566 , LYS A:573 , THR A:574 , TRP A:577 , FMN A:702 , HOH A:709 , HOH A:710 , HOH A:715 , HOH A:749 , HOH A:762 , HOH A:792 , HOH A:818 , HOH A:952 , HOH A:976 , HOH A:977 , HOH A:984 , HOH A:1045BINDING SITE FOR RESIDUE MDE A 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PS9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PS9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PS9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PS9)

(-) Exons   (0, 0)

(no "Exon" information available for 1PS9)

(-) 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:671
 aligned with FADH_ECOLI | P42593 from UniProtKB/Swiss-Prot  Length:672

    Alignment length:671
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671 
           FADH_ECOLI     2 SYPSLFAPLDLGFTTLKNRVLMGSMHTGLEEYPDGAERLAAFYAERARHGVALIVSGGIAPDLTGVGMEGGAMLNDASQIPHHRTITEAVHQEGGKIALQILHTGRYSYQPHLVAPSALQAPINRFVPHELSHEEILQLIDNFARCAQLAREAGYDGVEVMGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGATIINTGIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNRINDPQVADDILSRGDADMVSMARPFLADAELLSKAQSGRADEINTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVTLKLNHTVTADQLQAFDETILASGIVPRTPPIDGIDHPKVLSYLDVLRDKAPVGNKVAIIGCGGIGFDTAMYLSQPGESTSQNIAGFCNEWGIDSSLQQAGGLSPQGMQIPRSPRQIVMLQRKASKPGQGLGKTTGWIHRTTLLSRGVKMIPGVSYQKIDDDGLHVVINGETQVLAVDNVVICAGQEPNRALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 672
               SCOP domains d1ps9a1 A:1-330 2,4-dienoyl-CoA reductase, N-terminal domain                                                                                                                                                                                                                                                                              d1ps9a3 A:331-465,A:628-671 2,4-dienoyl-CoA reductase, middle domain                                                                   d1ps9a2 A:466-627 2,4-dienoyl-CoA reductase, C-terminal domain                                                                                                    d1ps9a3 A:331-465,A:628-671                  SCOP domains
               CATH domains 1ps9A01 A:1-368 Aldolase class I                                                                                                                                                                                                                                                                                                                                                1ps9A02 A:369-467,A:626-671 NAD(P)-binding Rossmann-like Domain                                    1ps9A03 A:468-624  [code=3.50.50.60, no name defined]                                                                                                        -1ps9A02 A:369-467,A:626-671                    CATH domains
               Pfam domains ---Oxidored_FMN-1ps9A02 A:4-330                                                                                                                                                                                                                                                                                                           --------------------------------------------Pyr_redox_2-1ps9A01 A:375-590                                                                                                                                                                                           --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee....ee...eee...........hhhhhhhhhhhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhh...eeeee..hhhhh.....ee.............ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.......hhhhhhhhhhhhhhhh..eeeeee..................hhhhhhhhh......eee.....hhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhhhhhh.........hhhhhhh...........................eeeee..hhhhhhhhhhhhh...eeeeee.......hhhhhh......hhhhhhhhhhhhhhhhh.eeee.............eeee...eee............eeehhhhhh.......eeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhh............eeeee..............hhhhhhhhhhhh..eee...eeeeee..eeeeee..eeeee...eeee...eee...hhhhhhh....eee.hhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ps9 A   1 SYPSLFAPLDLGFTTLKNRVLMGSMHTGLEEYPDGAERLAAFYAERARHGVALIVSGGIAPDLTGVGMEGGAMLNDASQIPHHRTITEAVHQEGGKIALQILHTGRYSYQPHLVAPSALQAPINRFVPHELSHEEILQLIDNFARCAQLAREAGYDGVEVMGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGATIINTGIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNRINDPQVADDILSRGDADMVSMARPFLADAELLSKAQSGRADEINTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGAGPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVTLKLNHTVTADQLQAFDETILASGIVPRTPPIDGIDHPKVLSYLDVLRDKAPVGNKVAIIGCGGIGFDTAMYLSQPGESTSQNIAGFCNEWGIDSSLQQAGGLSPQGMQIPRSPRQIVMLQRKASKPGQGLGKTTGWIHRTTLLSRGVKMIPGVSYQKIDDDGLHVVINGETQVLAVDNVVICAGQEPNRALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 671
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FADH_ECOLI | P42593)
molecular function
    GO:0008670    2,4-dienoyl-CoA reductase (NADPH) activity    Catalysis of the reaction: trans-2,3-didehydroacyl-CoA + NADP+ = trans,trans-2,3,4,5-tetradehydroacyl-CoA + NADPH + H+.
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0003959    NADPH dehydrogenase activity    Catalysis of the reaction: NADPH + H+ + acceptor = NADP+ + reduced acceptor.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0033543    fatty acid beta-oxidation, unsaturated, even number, reductase/isomerase pathway    A fatty acid beta-oxidation pathway by which fatty acids having cis-double bonds on even-numbered carbons are degraded. In this pathway, the intermediate 2,4-dienoyl-CoA is converted to trans-2-enoyl-CoA by 2,4-dienoyl-CoA reductase and delta3-delta2-enoyl-CoA isomerase; trans-2-enoyl-CoA returns to the core beta-oxidation pathway for further degradation. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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