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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DUTPASE R140K, H145W MUTANT
 
Authors :  G. N. Nagy, I. Leveles, A. Lopata, V. Harmat, J. Toth, G. B. Vertessy
Date :  21 Oct 15  (Deposition) - 02 Nov 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Jelly-Roll, Enzyme-Ligand Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. N. Nagy, R. Suardiaz, A. Lopata, O. Ozohanics, K. Vekey, B. R. Brooks I. Leveles, J. Toth, B. G. Vertessy, E. Rosta
Structural Characterization Of Arginine Fingers: Identification Of An Arginine Finger For The Pyrophosphatas Dutpases.
J. Am. Chem. Soc. V. 138 15035 2016
PubMed-ID: 27740761  |  Reference-DOI: 10.1021/JACS.6B09012

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    Chains: A
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DUT, MRA_2725
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: DUTPASE,DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1DUP3Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:74 , ILE A:75 , VAL A:76 , HOH A:354binding site for residue TRS A 201
2AC2SOFTWAREARG A:64 , SER A:65 , GLY A:66 , ASN A:77 , GLY A:80 , THR A:81 , ILE A:82 , ASP A:83 , TYR A:86 , GLU A:89 , ILE A:90 , LYS A:91 , GLN A:113 , MG A:203 , HOH A:302 , HOH A:304 , HOH A:310 , HOH A:313 , HOH A:316 , HOH A:322 , HOH A:323 , HOH A:326 , HOH A:330 , HOH A:334 , HOH A:348 , HOH A:351 , HOH A:377binding site for residue DUP A 202
3AC3SOFTWAREDUP A:202 , HOH A:313 , HOH A:322 , HOH A:377binding site for residue MG A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EDD)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh......eee.................eeee....eee....eeeee..eee.....eeeeee.hhhhhhhhheee....eeee.......eeeeee......eee....eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5edd A -10 HSSGLVPRGSHMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEA 133
                                    -1         9        19        29        39        49        59        69        79        89        99       109       119       129
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5EDD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EDD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EDD)

(-) Gene Ontology  (11, 19)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUT_MYCTU | P9WNS5: 1mq7 1six 1sjn 1slh 1sm8 1smc 1snf 2py4 3h6d 3hza 3i93 3loj 4gcy 5ect

(-) Related Entries Specified in the PDB File

2py4 2PY4 CONTAINS THE WILD-TYPE FORM OF THE SAME PROTEIN
3h6d 3H6D CONTAINS THE SAME PROTEIN WITH ANOTHER MUTATION
3hza 3HZA CONTAINS THE SAME PROTEIN WITH ANOTHER MUTATION
3i93 3I93 CONTAINS THE SAME PROTEIN WITH A C TERMINAL TRUNCATION
3loj 3LOJ CONTAINS THE SAME PROTEIN WITH ANOTHER MUTATION
4gcy 4GCY CONTAINS THE SAME PROTEIN WITH ANOTHER MUTATION