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(-) Description

Title :  THE STRUCTURE OF YEAST DELTA3-DELTA2-ENOYL-COA ISOMERASE COMPLEXED WITH OCTANOYL-COA
 
Authors :  A. M. Mursula, A. Geerlof, J. K. Hiltunen, R. K. Wierenga
Date :  02 Oct 01  (Deposition) - 05 Aug 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.29
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Beta-Beta-Alpha Spiral, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  

PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D3,D2-ENOYL COA ISOMERASE ECI1
    Chains: A, B, C
    EC Number: 5.3.3.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECI1
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CO83Ligand/IonOCTANOYL-COENZYME A
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CO86Ligand/IonOCTANOYL-COENZYME A
2PO46Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:225 , PRO A:227 , TYR B:258BINDING SITE FOR RESIDUE PO4 A 281
2AC2SOFTWARETYR B:225 , LYS C:257 , TYR C:258BINDING SITE FOR RESIDUE PO4 C 281
3AC3SOFTWARELYS A:257 , TYR A:258 , TYR C:225 , PRO C:227BINDING SITE FOR RESIDUE PO4 A 282
4AC4SOFTWAREASP A:28 , ASN A:29 , LEU A:30 , ALA A:32 , GLY A:35 , SER A:68 , ALA A:70 , ASP A:71 , PHE A:72 , PHE A:97 , ARG A:100 , ASN A:101 , ILE A:124 , GLY A:125 , LEU A:126 , LEU A:153 , GLU A:158BINDING SITE FOR RESIDUE CO8 A 300
5AC5SOFTWARELEU B:30 , ALA B:32 , SER B:68 , ALA B:70 , ASP B:71 , LYS B:73 , PHE B:97 , ARG B:100 , ASN B:101 , ILE B:124 , GLY B:125 , LEU B:126 , LEU B:153 , LEU B:155 , GLU B:158BINDING SITE FOR RESIDUE CO8 B 301
6AC6SOFTWAREASP C:28 , ASN C:29 , LEU C:30 , ALA C:32 , SER C:68 , ALA C:70 , ASP C:71 , PHE C:72 , LYS C:73 , PHE C:97 , ARG C:100 , ASN C:101 , ILE C:124 , GLY C:125 , LEU C:126 , LEU C:155 , GLU C:158BINDING SITE FOR RESIDUE CO8 C 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K39)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K39)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K39)

(-) Exons   (1, 3)

Asymmetric Unit (1, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR284C1YLR284C.1XII:707042-706200843ECI1_YEAST1-2802803A:4-272
B:4-274
C:5-270		269
271
266

(-) 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:269
 aligned with ECI1_YEAST | Q05871 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:269
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263         
           ECI1_YEAST     4 EIRQNEKISYRIEGPFFIIHLMNPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGIAKAQGDDTNKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRFRQLG 272
               SCOP domains d1k39a_ A: Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase)                                                                                                                                                                                                          SCOP domains
               CATH domains 1k39A00 A:4-272 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeee.........hhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...eehhhhhhhh...eeee.....eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh..eeee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-272 UniProt: 1-280 [INCOMPLETE]                                                                                                                                                                                                                            Transcript 1
                 1k39 A   4 EIRQNEKISYRIEGPFFIIHLINPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGIAKAQGDDTNKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRFRQLG 272
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263         


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with ECI1_YEAST | Q05871 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:271
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273 
           ECI1_YEAST     4 EIRQNEKISYRIEGPFFIIHLMNPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGIAKAQGDDTNKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRFRQLGSK 274
               SCOP domains d1k39b_ B: Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase)                                                                                                                                                                                                            SCOP domains
               CATH domains 1k39B00 B:4-274 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeee...........hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...eehhhhhhhhhh.eeee.....eee............hhhhhhhhhhhhhhhhhhhh....eehhhhhhh..eeee......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:4-274 UniProt: 1-280 [INCOMPLETE]                                                                                                                                                                                                                              Transcript 1
                 1k39 B   4 EIRQNEKISYRIEGPFFIIHLINPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGIAKAQGDDTNKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRFRQLGSK 274
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273 


Chain C from PDB  Type:PROTEIN  Length:266
 aligned with ECI1_YEAST | Q05871 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:266
                                    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      
           ECI1_YEAST     5 IRQNEKISYRIEGPFFIIHLMNPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGIAKAQGDDTNKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRFRQ 270
               SCOP domains d1k39c_ C: Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase)                                                                                                                                                                                                       SCOP domains
               CATH domains 1k39C00 C:5-270 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) -------ECH-1k39C01 C:12-258                                                                                                                                                                                                                                   ------------ Pfam domains (1)
           Pfam domains (2) -------ECH-1k39C02 C:12-258                                                                                                                                                                                                                                   ------------ Pfam domains (2)
           Pfam domains (3) -------ECH-1k39C03 C:12-258                                                                                                                                                                                                                                   ------------ Pfam domains (3)
         Sec.struct. author ......eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...eehhhhhhhh...eeee.....eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh..eeee......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:5-270 UniProt: 1-280 [INCOMPLETE]                                                                                                                                                                                                                         Transcript 1
                 1k39 C   5 IRQNEKISYRIEGPFFIIHLINPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGIAKAQGDDTNKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRFRQ 270
                                    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
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: ClpP_crotonase (88)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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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  1k39
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 Related Entries

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

UniProtKB/Swiss-Prot
        ECI1_YEAST | Q05871: 1hno 1hnu 1pjh 4zdb 4zdc 4zdd 4zde 4zdf

(-) Related Entries Specified in the PDB File

1hno CRYSTAL STRUCTURE OF PEROXISOMAL 3-2-ENOYL-COA ISOMERASE FROM SACCHAROMYCES CEREVISIAE
1hnu CRYSTAL STRUCTURE OF PEROXISOMAL 3-2-ENOYL-COA ISOMERASE FROM SACCHAROMYCES CEREVISIAE