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(-) Description

Title :  CRYSTAL STRUCTURE OF OSD14 IN COMPLEX WITH HYDROXY D-RING
 
Authors :  Y. -L. Xue, T. Miyakawa, F. Hou, H. -M. Qin, M. Tanokura
Date :  22 Sep 13  (Deposition) - 23 Oct 13  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta-Hydrolase Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Nakamura, Y. -L. Xue, T. Miyakawa, F. Hou, H. -M. Qin, K. Fukui, X. Shi E. Ito, S. Ito, S. -H. Park, Y. Miyauchi, A. Asano, N. Totsuka, T. Ueda, M. Tanokura, T. Asami
Molecular Mechanism Of Strigolactone Perception By Dwarf14
Nat Commun V. 4 2613 2013
PubMed-ID: 24131983  |  Reference-DOI: 10.1038/NCOMMS3613

(-) Compounds

Molecule 1 - PROBABLE STRIGOLACTONE ESTERASE D14
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 54-318
    Gene: D14, D88, HTD2, LOC_OS03G10620, OS03G0203200
    Organism Common: JAPONICA RICE
    Organism Scientific: ORYZA SATIVA JAPONICA GROUP
    Organism Taxid: 39947
    Synonym: DWARF 88 ESTERASE, PROTEIN DWARF-14, PROTEIN DWARF-88, PROTEIN HIGH-TILLERING DWARF 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1H3M1Ligand/Ion(5R)-5-HYDROXY-3-METHYLFURAN-2(5H)-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1H3M1Ligand/Ion(5R)-5-HYDROXY-3-METHYLFURAN-2(5H)-ONE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1H3M-1Ligand/Ion(5R)-5-HYDROXY-3-METHYLFURAN-2(5H)-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:186 , VAL A:194 , TRP A:205 , TYR A:209 , PHE A:245 , SER A:270BINDING SITE FOR RESIDUE H3M A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WIO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WIO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WIO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WIO)

(-) Exons   (0, 0)

(no "Exon" information available for 3WIO)

(-) 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:265
 aligned with D14_ORYSJ | Q10QA5 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:265
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313     
            D14_ORYSJ    54 AKLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeee....eeeee.....hhhhhh.hhhhh....eeee.........hhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh...eeeee.........hhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wio A  54 AKLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313     


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with D14_ORYSJ | Q10QA5 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:266
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312      
            D14_ORYSJ    53 GAKLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeee....eeeee.....hhhhhh..hhhhhh..eeee.........hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh...eeeee.........hhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wio B  53 SAKLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3WIO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WIO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WIO)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (D14_ORYSJ | Q10QA5)
molecular function
    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:0010223    secondary shoot formation    The process that gives rise to secondary (or auxiliary or axillary) shoots in plants. This process pertains to the initial formation of a structure from unspecified parts. These secondary shoots originate from secondary meristems initiated in the axils of leaf primordia. Axillary meristems function like the shoot apical meristem of the primary shoot initating the development of lateral organs.
    GO:1901601    strigolactone biosynthetic process    The chemical reactions and pathways resulting in the formation of strigolactone.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        D14_ORYSJ | Q10QA5: 3vxk 3w04 3w05 4ih9 4iha 5dj5

(-) Related Entries Specified in the PDB File

3vxk