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(-) Description

Title :  SOLUTION STRUCTURE OF THE PLANT HOMEODOMAIN (PHD) OF THE E3 SUMO LIGASE SIZ1 FROM RICE
 
Authors :  H. Shindo, W. Tsuchiya, R. Suzuki, T. Yamazaki
Date :  12 Jan 12  (Deposition) - 15 Aug 12  (Release) - 15 Aug 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  E3 Sumo Ligase, Plant Homeodomain (Phd), Histone Binding, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Shindo, R. Suzuki, W. Tsuchiya, M. Taichi, Y. Nishiuchi, T. Yamazak
Phd Finger Of The Sumo Ligase Siz/Pias Family In Rice Reveals Specific Binding For Methylated Histone H3 At Lysin 4 And Arginine 2
Febs Lett. V. 586 1783 2012
PubMed-ID: 22626555  |  Reference-DOI: 10.1016/J.FEBSLET.2012.04.063

(-) Compounds

Molecule 1 - E3 SUMO-PROTEIN LIGASE SIZ1
    Chains: A
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector: PGEX-4T-3
    Expression System Vector Type: VECTOR
    Fragment: PLANT HOMEODOMAIN, UNP RESIDUES 107-172
    Gene: SIZ1, OS05G0125000, LOC_OS05G03430, OSJNBB0079L11.3
    Organism Common: JAPANESE RICE
    Organism Scientific: ORYZA SATIVA JAPONICA GROUP
    Organism Taxid: 39947

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:117 , CYS A:119 , HIS A:141 , CYS A:144BINDING SITE FOR RESIDUE ZN A 901
2AC2SOFTWARECYS A:131 , CYS A:136 , VAL A:138 , CYS A:163 , CYS A:166BINDING SITE FOR RESIDUE ZN A 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_1PS01359 Zinc finger PHD-type signature.SIZ1_ORYSJ117-166  1A:117-166
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_1PS01359 Zinc finger PHD-type signature.SIZ1_ORYSJ117-166  1A:117-166

(-) Exons   (0, 0)

(no "Exon" information available for 2RSD)

(-) Sequences/Alignments

NMR Structure
   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:68
 aligned with SIZ1_ORYSJ | Q6L4L4 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:79
                                   103       113       123       133       143       153       163         
           SIZ1_ORYSJ    94 GSDFSFRPIEEAYDSFQPEAKVRCICSSTMVNDSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRLSRAD 172
               SCOP domains d2           rsda_ A: automated matches                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------.......ee............eee.......eeee.....................hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------ZF_PHD_1  PDB: A:117-166 UniProt: 117-166         ------ PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 2rsd A 105 GS-----------DSFQPEAKVRCICSSTMVNDSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRLSRAD 172
                             |       -   |   113       123       133       143       153       163         
                             |         107                                                                 
                           106
   Legend:   → Mismatch (orange background)
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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  (1, 1)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (SIZ1_ORYSJ | Q6L4L4)
molecular function
    GO:0061665    SUMO ligase activity    Catalysis of the transfer of SUMO to a substrate protein via the reaction X-SUMO + S --> X + S-SUMO, where X is either an E2 or E3 enzyme, the X-SUMO linkage is a thioester bond, and the S-SUMO linkage is an isopeptide bond between the C-terminal amino acid of SUMO and the epsilon-amino group of lysine residues in the substrate.
    GO:0019789    SUMO transferase activity    Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0031668    cellular response to extracellular stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
    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

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        SIZ1_ORYSJ | Q6L4L4: 2rno

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