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(-) Description

Title :  CRYSTAL STRUCTURE OF PEROXISOMAL DELTA3-DELTA2-ENOYL-COA ISOMERASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  A. M. Mursula, D. M. F. Van Aalten, J. K. Hiltunen, R. K. Wierenga
Date :  08 Dec 00  (Deposition) - 20 Jun 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Biol. Unit 2:  A  (3x)
Keywords :  Alpha/Beta, Unliganded, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. M. Mursula, D. M. Van Aalten, J. K. Hiltunen, R. K. Wierenga
The Crystal Structure Of Delta(3)-Delta(2)-Enoyl-Coa Isomerase.
J. Mol. Biol. V. 309 845 2001
PubMed-ID: 11399063  |  Reference-DOI: 10.1006/JMBI.2001.4671
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D3,D2-ENOYL COA ISOMERASE ECI1
    ChainsA
    EC Number5.3.3.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (6x)A
Biological Unit 2 (3x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:133 , CYS A:134 , LYS A:168 , PHE A:244 , HOH A:308 , HOH A:309 , HOH A:457BINDING SITE FOR RESIDUE EDO A 281
2AC2SOFTWAREARG A:64 , ASN A:141 , LYS A:143 , PRO A:202 , SER A:203BINDING SITE FOR RESIDUE EDO A 282

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR284C1YLR284C.1XII:707042-706200843ECI1_YEAST1-2802801A:8-270 (gaps)263

(-) Sequences/Alignments

Asymmetric 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:248
 aligned with ECI1_YEAST | Q05871 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:263
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267   
           ECI1_YEAST     8 NEKISYRIEGPFFIIHLMNPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGIAKAQGDDTNKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRFRQ 270
               SCOP domains d1hnoa_ A: Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomeras               e)                                                                                                                                                                                     SCOP domains
               CATH domains 1hnoA00 A:8-270 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeee.............---------------....hhhhhhhhhhhhhhhhhhh..eeeeee...eehhhhhhhh...eeee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhh...eehhhhhhh....ee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:8-270 (gaps) UniProt: 1-280 [INCOMPLETE]                                                                                                                                                                                                               Transcript 1
                 1hno A   8 NEKISYRIEGPFFIIHLINPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFK---------------ETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRFRQ 270
                                    17        27        37        47        57        67     |   -         - |      97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267   
                                                                                            73              89                                                                                                                                                                                     

   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HNO)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (ECI1_YEAST | Q05871)
molecular function
    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:0004165    dodecenoyl-CoA delta-isomerase activity    Catalysis of the reaction: 3-cis-dodecenoyl-CoA = 2-trans-dodecenoyl-CoA.
    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.
biological process
    GO:0006635    fatty acid beta-oxidation    A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ECI1_YEAST | Q058711hnu 1k39 1pjh 4zdb 4zdc 4zdd 4zde 4zdf

(-) Related Entries Specified in the PDB File

1hnu 1HNU IS THE LIGANDED STRUCTURE