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(-) Description

Title :  CRYSTAL STRUCTURE OF CUTA1 FROM ORYZA SATIVA
 
Authors :  Y. Kezuka, B. Bagautdinov, S. Katoh, Y. Ohtake, K. Yutani, T. Nonaka, E.
Date :  23 May 08  (Deposition) - 26 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Trimeric Structure, Protein Stability, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kezuka, B. Bagautdinov, S. Katoh, Y. Ohtake, K. Yutani, T. Nonaka, E. Katoh
Crystal Structure Of Cuta1 From Oryza Sativa
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN CUTA, CHLOROPLAST, PUTATIVE, EXPRESSED
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST-HIS VECTOR
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 65-177
    Organism Common: JAPANESE RICE
    Organism Scientific: ORYZA SATIVA SUBSP. JAPONICA
    Organism Taxid: 39947
    Synonym: CUTA1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:33 , HIS A:78 , ALA A:81 , ASN A:82BINDING SITE FOR RESIDUE GOL A 115
2AC2SOFTWARETHR A:7 , VAL A:8 , PRO A:9 , SER A:10 , ILE A:95 , GLY A:97 , LEU A:103BINDING SITE FOR RESIDUE SO4 A 114
3AC3SOFTWARELYS A:101 , TRP B:50 , GLU B:52 , GLY B:53BINDING SITE FOR RESIDUE GOL B 115
4AC4SOFTWAREPRO B:9 , SER B:10 , ILE B:95 , LYS B:96 , GLY B:97BINDING SITE FOR RESIDUE SO4 B 114
5AC5SOFTWAREGLU C:33 , HIS C:78 , ALA C:81 , ASN C:82BINDING SITE FOR RESIDUE GOL C 115
6AC6SOFTWAREVAL C:8 , PRO C:9 , SER C:10 , ILE C:95 , GLY C:97BINDING SITE FOR RESIDUE SO4 C 114

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZOM)

(-) 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:107
 aligned with CUTA1_ORYSJ | Q109R6 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:107
                                    78        88        98       108       118       128       138       148       158       168       
          CUTA1_ORYSJ    69 STTVPSIVVYVTVPNKEAGKRLAGSIISEKLAACVNIVPGIESVYWWEGKVQTDAEELLIIKTRESLLDALTEHVKANHEYDVPEVIALPIKGGNLKYLEWLKNSTR 175
               SCOP domains d2zoma_ A: automated matches                                                                                SCOP domains
               CATH domains 2zomA00 A:5-111  [code=3.30.70.830, no name defined]                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeeeeeeee..eeeeeeeeeeeeeee..hhhhhhhhhhhh........eeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2zom A   5 STTVPSIVVYVTVPNKEAGKRLAGSIISEKLAACVNIVPGIESVYWWEGKVQTDAEELLIIKTRESLLDALTEHVKANHEYDVPEVIALPIKGGNLKYLEWLKNSTR 111
                                    14        24        34        44        54        64        74        84        94       104       


Chain B from PDB  Type:PROTEIN  Length:108
 aligned with CUTA1_ORYSJ | Q109R6 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:108
                                    79        89        99       109       119       129       139       149       159       169        
          CUTA1_ORYSJ    70 TTVPSIVVYVTVPNKEAGKRLAGSIISEKLAACVNIVPGIESVYWWEGKVQTDAEELLIIKTRESLLDALTEHVKANHEYDVPEVIALPIKGGNLKYLEWLKNSTRES 177
               SCOP domains d2zomb_ B: automated matches                                                                                 SCOP domains
               CATH domains 2zomB00 B:6-113  [code=3.30.70.830, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhhhhhhh........eeee....hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2zom B   6 TTVPSIVVYVTVPNKEAGKRLAGSIISEKLAACVNIVPGIESVYWWEGKVQTDAEELLIIKTRESLLDALTEHVKANHEYDVPEVIALPIKGGNLKYLEWLKNSTRES 113
                                    15        25        35        45        55        65        75        85        95       105        


Chain C from PDB  Type:PROTEIN  Length:109
 aligned with CUTA1_ORYSJ | Q109R6 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:109
                                    78        88        98       108       118       128       138       148       158       168         
          CUTA1_ORYSJ    69 STTVPSIVVYVTVPNKEAGKRLAGSIISEKLAACVNIVPGIESVYWWEGKVQTDAEELLIIKTRESLLDALTEHVKANHEYDVPEVIALPIKGGNLKYLEWLKNSTRES 177
               SCOP domains d2zomc_ C: automated matches                                                                                  SCOP domains
               CATH domains 2zomC00 C:5-113  [code=3.30.70.830, no name defined]                                                          CATH domains
           Pfam domains (1) -----CutA1-2zomC01 C:10-111                                                                                -- Pfam domains (1)
           Pfam domains (2) -----CutA1-2zomC02 C:10-111                                                                                -- Pfam domains (2)
           Pfam domains (3) -----CutA1-2zomC03 C:10-111                                                                                -- Pfam domains (3)
         Sec.struct. author .....eeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeeeeeeee..eeeeeeeeeeeeeee..hhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2zom C   5 STTVPSIVVYVTVPNKEAGKRLAGSIISEKLAACVNIVPGIESVYWWEGKVQTDAEELLIIKTRESLLDALTEHVKANHEYDVPEVIALPIKGGNLKYLEWLKNSTRES 113
                                    14        24        34        44        54        64        74        84        94       104
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: GlnB-like (50)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CUTA1_ORYSJ | Q109R6)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
biological process
    GO:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
    GO:0010038    response to metal ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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