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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL DELTA3-DELTA2-ENOYL-COA ISOMERASE
 
Authors :  S. T. Partanen, D. K. Novikov, A. N. Popov, A. M. Mursula, J. K. Hiltunen, R. K. Wierenga
Date :  23 Feb 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Crotonase Fold, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. T. Partanen, D. K. Novikov, A. N. Popov, A. M. Mursula, J. K. Hiltunen, R. K. Wierenga
The 1. 3 A Crystal Structure Of Human Mitochondrial Delta3-Delta2-Enoyl-Coa Isomerase Shows A Novel Mode Of Binding For The Fatty Acyl Group.
J. Mol. Biol. V. 342 1197 2004
PubMed-ID: 15351645  |  Reference-DOI: 10.1016/J.JMB.2004.07.039
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3,2-TRANS-ENOYL-COA ISOMERASE, MITOCHONDRIAL
    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: DCI
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DODECENOYL-COA DELTA-ISOMERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CO81Ligand/IonOCTANOYL-COENZYME A
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CO81Ligand/IonOCTANOYL-COENZYME A
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CO82Ligand/IonOCTANOYL-COENZYME A

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:24 , VAL B:25 , VAL B:61 , ALA B:64 , LEU B:66 , ASP B:67 , LEU B:68 , PRO B:109 , ALA B:110 , GLY B:111 , ASN B:135 , ILE B:142 , TYR B:251 , LEU B:255 , LYS B:256 , LYS B:259BINDING SITE FOR RESIDUE CO8 B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SG4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:23 -Pro A:24
2Pro B:23 -Pro B:24
3Pro C:23 -Pro C:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SG4)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENOYL_COA_HYDRATASEPS00166 Enoyl-CoA hydratase/isomerase signature.ECI1_HUMAN143-163
 
 		  3A:101-121
B:101-121
C:101-121
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENOYL_COA_HYDRATASEPS00166 Enoyl-CoA hydratase/isomerase signature.ECI1_HUMAN143-163
 
 		  3A:101-121
B:101-121
C:101-121
Biological Unit 2 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENOYL_COA_HYDRATASEPS00166 Enoyl-CoA hydratase/isomerase signature.ECI1_HUMAN143-163
 
 		  6A:101-121
B:101-121
C:101-121

(-) Exons   (6, 18)

Asymmetric Unit (6, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003017291ENSE00001197484chr16:2301615-2301516100ECI1_HUMAN1-18180--
1.2ENST000003017292ENSE00001118809chr16:2301430-2301317114ECI1_HUMAN18-56393A:2-14
B:3-14
C:3-14		13
12
12
1.3ENST000003017293ENSE00001118808chr16:2296987-2296860128ECI1_HUMAN56-98433A:14-56
B:14-56
C:14-56		43
43
43
1.4ENST000003017294ENSE00001118811chr16:2294553-2294407147ECI1_HUMAN99-147493A:57-105
B:57-105
C:57-105		49
49
49
1.5ENST000003017295ENSE00001118813chr16:2293440-2293319122ECI1_HUMAN148-188413A:106-146
B:106-146
C:106-146		41
41
41
1.6ENST000003017296ENSE00001118810chr16:2293225-2293047179ECI1_HUMAN188-248613A:146-206
B:146-206
C:146-206		61
61
61
1.7ENST000003017297ENSE00001118812chr16:2290146-2289396751ECI1_HUMAN248-302553A:206-250
B:206-260
C:206-252		45
55
47

(-) 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:249
 aligned with ECI1_HUMAN | P42126 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:249
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
           ECI1_HUMAN    44 SQRVLVEPDAGAGVAVMKFKNPPVNSLSLEFLTELVISLEKLENDKSFRGVILTSDRPGVFSAGLDLTEMCGRSPAHYAGYWKAVQELWLRLYQSNLVLVSAINGACPAGGCLVALTCDYRILADNPRYCIGLNETQLGIIAPFWLKDTLENTIGHRAAERALQLGLLFPPAEALQVGIVDQVVPEEQVQSTALSAIAQWMAIPDHARQLTKAMMRKATASRLVTQRDADVQNFVSFISKDSIQKSLQM 292
               SCOP domains d1sg4a1 A:2-250 Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase)                                                                                                                                                                                 SCOP domains
               CATH domains 1sg4A01 A:2-204 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                   ---------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeeee......eehhhhhhhhhhhhhhhhhh....eeeeee...ee...ee.hhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeee.ee.hhhhhhhhh...eeeee.........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  --------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2     ------------------------------------------Exon 1.4  PDB: A:57-105 UniProt: 99-147          Exon 1.5  PDB: A:106-146 UniProt: 148-188-----------------------------------------------------------Exon 1.7  PDB: A:206-250 UniProt: 248-302     Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3  PDB: A:14-56 UniProt: 56-98      -----------------------------------------------------------------------------------------Exon 1.6  PDB: A:146-206 UniProt: 188-248                    -------------------------------------------- Transcript 1 (2)
                 1sg4 A   2 SQRVLVEPDAGAGVAVMKFKNPPVNSLSLEFLTELVISLEKLENDKSFRGVILTSDRPGVFSAGLDLTEMCGRSPAHYAGYWKAVQELWLRLYQSNLVLVSAINGACPAGGCLVALTCDYRILADNPRYCIGLNETQLGIIAPFWLKDTLENTIGHRAAERALQLGLLFPPAEALQVGIVDQVVPEEQVQSTALSAIAQWMAIPDHARQLTKAMMRKATASRLVTQRDADVQNFVSFISKDSIQKSLQM 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with ECI1_HUMAN | P42126 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:258
                                    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        
           ECI1_HUMAN    45 QRVLVEPDAGAGVAVMKFKNPPVNSLSLEFLTELVISLEKLENDKSFRGVILTSDRPGVFSAGLDLTEMCGRSPAHYAGYWKAVQELWLRLYQSNLVLVSAINGACPAGGCLVALTCDYRILADNPRYCIGLNETQLGIIAPFWLKDTLENTIGHRAAERALQLGLLFPPAEALQVGIVDQVVPEEQVQSTALSAIAQWMAIPDHARQLTKAMMRKATASRLVTQRDADVQNFVSFISKDSIQKSLQMYLERLKEEKG 302
               SCOP domains d1sg4b_ B: Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase)                                                                                                                                                                                               SCOP domains
               CATH domains 1sg4B01 B:3-204 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                  -------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....eeeeee........hhhhhhhhhhhhhhhhhh....eeeeee...ee.....hhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeee.ee.hhhhhhhhhhh.eeeee.........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2    ------------------------------------------Exon 1.4  PDB: B:57-105 UniProt: 99-147          Exon 1.5  PDB: B:106-146 UniProt: 148-188-----------------------------------------------------------Exon 1.7  PDB: B:206-260 UniProt: 248-302               Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.3  PDB: B:14-56 UniProt: 56-98      -----------------------------------------------------------------------------------------Exon 1.6  PDB: B:146-206 UniProt: 188-248                    ------------------------------------------------------ Transcript 1 (2)
                 1sg4 B   3 QRVLVEPDAGAGVAVMKFKNPPVNSLSLEFLTELVISLEKLENDKSFRGVILTSDRPGVFSAGLDLTEMCGRSPAHYAGYWKAVQELWLRLYQSNLVLVSAINGACPAGGCLVALTCDYRILADNPRYCIGLNETQLGIIAPFWLKDTLENTIGHRAAERALQLGLLFPPAEALQVGIVDQVVPEEQVQSTALSAIAQWMAIPDHARQLTKAMMRKATASRLVTQRDADVQNFVSFISKDSIQKSLQMYLERLKEEKG 260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        


Chain C from PDB  Type:PROTEIN  Length:250
 aligned with ECI1_HUMAN | P42126 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:250
                                    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
           ECI1_HUMAN    45 QRVLVEPDAGAGVAVMKFKNPPVNSLSLEFLTELVISLEKLENDKSFRGVILTSDRPGVFSAGLDLTEMCGRSPAHYAGYWKAVQELWLRLYQSNLVLVSAINGACPAGGCLVALTCDYRILADNPRYCIGLNETQLGIIAPFWLKDTLENTIGHRAAERALQLGLLFPPAEALQVGIVDQVVPEEQVQSTALSAIAQWMAIPDHARQLTKAMMRKATASRLVTQRDADVQNFVSFISKDSIQKSLQMYL 294
               SCOP domains d1sg4c_ C: Dienoyl-CoA isomerase (delta3-delta2-enoyl-CoA isomerase)                                                                                                                                                                                       SCOP domains
               CATH domains 1sg4C01 C:3-204 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                  ------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeeee...ee.....hhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeee.ee.hhhhhhhhhhh.eeeee.........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2    ------------------------------------------Exon 1.4  PDB: C:57-105 UniProt: 99-147          Exon 1.5  PDB: C:106-146 UniProt: 148-188-----------------------------------------------------------Exon 1.7  PDB: C:206-252 UniProt: 248-302       Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.3  PDB: C:14-56 UniProt: 56-98      -----------------------------------------------------------------------------------------Exon 1.6  PDB: C:146-206 UniProt: 188-248                    ---------------------------------------------- Transcript 1 (2)
                 1sg4 C   3 QRVLVEPDAGAGVAVMKFKNPPVNSLSLEFLTELVISLEKLENDKSFRGVILTSDRPGVFSAGLDLTEMCGRSPAHYAGYWKAVQELWLRLYQSNLVLVSAINGACPAGGCLVALTCDYRILADNPRYCIGLNETQLGIIAPFWLKDTLENTIGHRAAERALQLGLLFPPAEALQVGIVDQVVPEEQVQSTALSAIAQWMAIPDHARQLTKAMMRKATASRLVTQRDADVQNFVSFISKDSIQKSLQMYL 252
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
   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  (2, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SG4)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (ECI1_HUMAN | P42126)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016860    intramolecular oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor are the same molecule, and no oxidized product appears.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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