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(-) Description

Title :  CRYSTAL STRUCTURE OF ORYZA SATIVA DWARF14 (D14)
 
Authors :  M. Kagiyama, Y. Hirano, T. Mori, S. Y. Kim, J. Kyozuka, Y. Seto, S. Yamagu T. Hakoshima
Date :  19 Oct 12  (Deposition) - 23 Jan 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Strigolactone Signaling, Alpha/Beta Hydrolase, Strigolactone Hydrolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kagiyama, Y. Hirano, T. Mori, S. Y. Kim, J. Kyozuka, Y. Seto, S. Yamaguchi, T. Hakoshima
Structures Of D14 And D14L In The Strigolactone And Karriki Signaling Pathways
Genes Cells V. 18 147 2013
PubMed-ID: 23301669  |  Reference-DOI: 10.1111/GTC.12025

(-) Compounds

Molecule 1 - DWARF 88 ESTERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET47B
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 55-318
    Gene: D88, LOC_OS03G10620, OS03G0203200
    Organism Common: JAPANESE RICE
    Organism Scientific: ORYZA SATIVA JAPONICA GROUP
    Organism Taxid: 39947
    Synonym: HYDROLASE, ALPHA/BETA FOLD FAMILY PROTEIN, EXPRESSED, OS03G0203200 PROTEIN

 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:209 , SER A:270 , HOH A:652 , HOH A:680 , HOH A:701BINDING SITE FOR RESIDUE MPD A 401
02AC2SOFTWARETYR A:182 , HIS A:183 , SER A:274 , VAL A:275BINDING SITE FOR RESIDUE EDO A 402
03AC3SOFTWAREMET A:198 , GLY A:199 , ASN A:201 , TYR A:202 , PRO A:234 , HOH A:512 , PRO B:90 , ARG B:312BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWAREALA A:303 , PRO A:304 , SER A:305 , LEU A:306BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREPHE A:230 , ALA B:216 , THR B:294 , GLU B:295 , SER B:302 , ALA B:303 , PRO B:304 , SER B:305 , LEU B:306 , HOH B:646 , HOH B:667 , HOH B:703 , HOH B:712BINDING SITE FOR RESIDUE EPE B 401
06AC6SOFTWARETYR B:209 , SER B:270 , HOH B:629 , HOH B:658BINDING SITE FOR RESIDUE MPD B 402
07AC7SOFTWAREASP B:181 , TYR B:182 , HIS B:183 , SER B:274 , VAL B:275 , HOH B:718BINDING SITE FOR RESIDUE EDO B 403
08AC8SOFTWAREASP B:120 , HIS B:239 , GLN B:242 , THR B:243BINDING SITE FOR RESIDUE EDO B 404
09AC9SOFTWAREGLN A:309 , ARG A:312 , ASP B:112 , ARG B:233 , HOH B:523BINDING SITE FOR RESIDUE EDO B 405
10BC1SOFTWAREGLY B:185 , ARG B:267 , ASP B:268 , VAL B:269 , VAL B:271 , PRO B:272 , LYS B:280BINDING SITE FOR RESIDUE EDO B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W04)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W04)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W04)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W04)

(-) Exons   (0, 0)

(no "Exon" information available for 3W04)

(-) 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:264
 aligned with D14_ORYSJ | Q10QA5 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:264
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314    
            D14_ORYSJ    55 KLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh..eeee....eeeee.....hhhhhh.hhhhh....eeee.........hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhh...eeeee........hhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w04 A  55 KLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALARY 318
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314    


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with D14_ORYSJ | Q10QA5 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:263
                                    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 AKLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALA 316
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeee....eeeee.....hhhhhh.hhhhh....eeee.........hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh...eeeee.........hhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w04 B  54 PKLLQILNVRVVGSGERVVVLSHGFGTDQSAWSRVLPYLTRDHRVVLYDLVCAGSVNPDHFDFRRYDNLDAYVDDLLAILDALRIPRCAFVGHSVSAMIGILASIRRPDLFAKLVLIGASPRFLNDSDYHGGFELEEIQQVFDAMGANYSAWATGYAPLAVGADVPAAVQEFSRTLFNMRPDISLHVCQTVFKTDLRGVLGMVRAPCVVVQTTRDVSVPASVAAYLKAHLGGRTTVEFLQTEGHLPHLSAPSLLAQVLRRALA 316
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 3W04)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W04)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W04)

(-) 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 3w05 3wio 4ih9 4iha 5dj5

(-) Related Entries Specified in the PDB File

3wo6