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(-) Description

Title :  APO-DUTPASE FROM ARABIDOPSIS THALIANA
 
Authors :  N. Inoguchi, M. Bajaj, H. Moriyama
Date :  03 Feb 14  (Deposition) - 22 Jul 15  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dutpase, Hydrolysis, Dutp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Inoguchi, K. Chaiseeda, M. Yamanishi, M. K. Kim, Y. Jang, M. Bajaj, C. P. Chia, D. F. Becker, H. Moriyama
Structural Insights Into The Mechanism Defining Substrate Affinity In Arabidopsis Thaliana Dutpase: The Role Of Tryptophan 93 In Ligand Orientation.
Bmc Res Notes V. 8 784 2015
PubMed-ID: 26666293  |  Reference-DOI: 10.1186/S13104-015-1760-1

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    Chains: A, B, C
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DUT, DUT1, AT3G46940, T6H20.30
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: DUTPASE, DUTP PYROPHOSPHATASE, DUTP-PYROPHOSPHATASE-LIKE 1, ATDUT1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:139 , LYS B:139 , LYS C:139BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWAREGLU A:138 , HOH A:386 , GLU B:138 , GLU C:138BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREARG A:64 , HIS A:119 , HOH A:414 , ARG B:64 , HIS B:119 , ARG C:64 , HIS C:119BINDING SITE FOR RESIDUE SO4 C 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OOQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OOQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OOQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OOQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4OOQ)

(-) 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:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheeee..ee.......eeeeeee.....eee....eeeeeeeeeee...eee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ooq A  26 SPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLSIAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADFEVKFGDRIAQLIIEKIVTPDVVEVDDLDETVR 156
                                    35        45        55        65        75        85        95       105       115       125       135       145       155 


Chain B from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee........ee.......eeee....eee....eeeee..eeee....eeeeee.hhhhhhhhheeeee.ee........eeeeee.....eee....eeeeeeeeeee...eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ooq B  25 PSPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLSIAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADFEVKFGDRIAQLIIEKIVTPDVVEVDDLDET 154
                                    34        44        54        64        74        84        94       104       114       124       134       144       154


Chain C from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee........ee.......eeee....eee....eeeee..eeee....eeeeee.hhhhhhhhheeee..ee........eeeeee.....eee....eeeeeeeeeee....ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ooq C  26 SPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLSIAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADFEVKFGDRIAQLIIEKIVTPDVVEVDDLD 152
                                    35        45        55        65        75        85        95       105       115       125       135       145
   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  (0, 0 ; only for superseded entry 2P9O: 1,3)

(no "SCOP Domain" information available for 4OOQ, only for superseded entry 2P9O replaced by 4OOQ)

(-) CATH Domains  (0, 0 ; only for superseded entry 2P9O: 1,3)

(no "CATH Domain" information available for 4OOQ, only for superseded entry 2P9O replaced by 4OOQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OOQ)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUT_ARATH | Q9STG6: 2pc5 4oop

(-) Related Entries Specified in the PDB File

4oop