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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN THIOESTERASE SUPERFAMILY MEMBER 2 (CASP TARGET)
 
Authors :  D. J. Ogg, J. Uppenberg, C. Arrowsmith, H. Berglund, A. Edwards, M. Ehn, S. Grasslund, S. Flodin, M. Hammerstrom, M. Hogbom, L. Holmberg- Schiavone, T. Kotenyova, P. Nilsson-Ehle, P. Nordlund, T. Nyman, C. Persson, J. Sagemark, M. Sundstrom, A. -G. Thorsell, J. Weigelt, M. Hallberg, Structural Genomics Consortium (Sgc)
Date :  25 May 06  (Deposition) - 20 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Thioesterase, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Ogg, J. Uppenberg, C. Arrowsmith, H. Berglund, A. Edwards, M. Ehn, S. Grasslund, S. Flodin, M. Hammerstrom, M. Hogbom, L. Holmberg-Schiavone, T. Kotenyova, P. Nilsson-Ehle, P. Nordlund, T. Nyman, C. Persson, J. Sagemark, M. Sundstrom, A. -G. Thorsell, J. Weigelt, M. Hallberg
The Crystal Structure Of Human Thioesterase Superfamily Member 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOESTERASE SUPERFAMILY MEMBER 2
    Chains: A, B, C, D
    EC Number: 3.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNIC-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 19-140
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2H4U)

(-) Sites  (0, 0)

(no "Site" information available for 2H4U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H4U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H4U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H4U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H4U)

(-) Exons   (3, 12)

Asymmetric/Biological Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002300481ENSE00001174688chr6:24667299-24667572274ACO13_HUMAN1-27274A:19-27
B:19-27
C:19-27
D:10-27 (gaps)		9
9
9
23
1.3ENST000002300483ENSE00001968027chr6:24698111-24698295185ACO13_HUMAN28-89624A:28-89
B:28-89
C:28-89
D:28-89		62
62
62
62
1.4ENST000002300484ENSE00001960410chr6:24701687-24701942256ACO13_HUMAN89-140524A:89-139
B:89-139
C:89-139
D:89-139		51
51
51
51

(-) 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:121
 aligned with ACO13_HUMAN | Q9NPJ3 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:121
                                    28        38        48        58        68        78        88        98       108       118       128       138 
          ACO13_HUMAN    19 RNFERVLGKITLVSAAPGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCTERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKHLG 139
               SCOP domains d2h4ua1 A:19-139 Hypothetical protein Them2                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhh.......eeeeeeeee........eeeeeeeeeee...eeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1 Exon 1.3  PDB: A:28-89 UniProt: 28-89                         -------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.4  PDB: A:89-139 UniProt: 89-140             Transcript 1 (2)
                 2h4u A  19 RNFERVLGKITLVSAAPGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCTERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKHLG 139
                                    28        38        48        58        68        78        88        98       108       118       128       138 


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with ACO13_HUMAN | Q9NPJ3 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:121
                                    28        38        48        58        68        78        88        98       108       118       128       138 
          ACO13_HUMAN    19 RNFERVLGKITLVSAAPGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCTERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKHLG 139
               SCOP domains d2h4ub_ B: Hypothetical protein Them2                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhh.......eeeeeeeee........eeeeeeeeeee...eeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1 Exon 1.3  PDB: B:28-89 UniProt: 28-89                         -------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.4  PDB: B:89-139 UniProt: 89-140             Transcript 1 (2)
                 2h4u B  19 RNFERVLGKITLVSAAPGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCTERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKHLG 139
                                    28        38        48        58        68        78        88        98       108       118       128       138 


Chain C from PDB  Type:PROTEIN  Length:121
 aligned with ACO13_HUMAN | Q9NPJ3 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:121
                                    28        38        48        58        68        78        88        98       108       118       128       138 
          ACO13_HUMAN    19 RNFERVLGKITLVSAAPGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCTERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKHLG 139
               SCOP domains d2h4uc_ C: Hypothetical protein Them2                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhh.......eeeeeeeee........eeeeeeeeeee...eeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1 Exon 1.3  PDB: C:28-89 UniProt: 28-89                         -------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.4  PDB: C:89-139 UniProt: 89-140             Transcript 1 (2)
                 2h4u C  19 RNFERVLGKITLVSAAPGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCTERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKHLG 139
                                    28        38        48        58        68        78        88        98       108       118       128       138 


Chain D from PDB  Type:PROTEIN  Length:130
 aligned with ACO13_HUMAN | Q9NPJ3 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:135
                                    14        24        34        44        54        64        74        84        94       104       114       124       134     
          ACO13_HUMAN     5 TQSLREVIKAMTKARNFERVLGKITLVSAAPGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCTERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKHLG 139
               SCOP domains d2h4  ud_ D   : Hypothetical protein Them2                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee--e.hhh---.hhhhhh.eeeeeeee..eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhh.......eeeeeeeee........eeeeeeeeeee...eeeeeeeeee.....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1 UniProt: 1-27 Exon 1.3  PDB: D:28-89 UniProt: 28-89                         -------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------Exon 1.4  PDB: D:89-139 UniProt: 89-140             Transcript 1 (2)
                 2h4u D  10 TENL--YFQSM---RNFERVLGKITLVSAAPGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCTERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKHLG 139
                               |  | 17|   |   24        34        44        54        64        74        84        94       104       114       124       134     
                              13 14  18  19
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H4U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H4U)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (ACO13_HUMAN | Q9NPJ3)
molecular function
    GO:0047617    acyl-CoA hydrolase activity    Catalysis of the reaction: acyl-CoA + H2O = CoA + a carboxylate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0035338    long-chain fatty-acyl-CoA biosynthetic process    The chemical reactions and pathways resulting in the formation of a long-chain fatty-acyl-CoA any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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: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.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

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        ACO13_HUMAN | Q9NPJ3: 2f0x 3f5o

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