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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS URACIL-DNA GLYCOSYLASE IN COMPLEX WITH 6-AMINOURACIL, FORM I
 
Authors :  S. M. Arif, K. Geethanandan, P. Mishra, A. Surolia, U. Varshney, M. Vija
Date :  25 Oct 14  (Deposition) - 15 Jul 15  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.13
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna-Repair, Excision Repair, Conformational Selection, Ligand- Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Arif, K. Geethanandan, P. Mishra, A. Surolia, U. Varshney, M. Vijayan
Structural Plasticity In Mycobacterium Tuberculosis Uracil-Dna Glycosylase (Mtung) And Its Functional Implications.
Acta Crystallogr. , Sect. D V. 71 1514 2015
PubMed-ID: 26143923  |  Reference-DOI: 10.1107/S1399004715009311
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETB MTUUDG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: UNG, RV2976C, MTCY349.11
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
    Synonym: UDG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
16UA1Ligand/Ion6-AMINOPYRIMIDINE-2,4(3H,5H)-DIONE
2CIT2Ligand/IonCITRIC ACID
3CL1Ligand/IonCHLORIDE ION
4DMS5Ligand/IonDIMETHYL SULFOXIDE
5IPA1Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:58 , THR A:72 , PRO A:91 , ARG A:92 , SER A:93 , ALA A:160 , 6UA A:303 , HOH A:421 , HOH A:425 , HOH A:431 , HOH A:433 , HOH A:444binding site for residue CIT A 301
02AC2SOFTWAREGLN A:67 , GLY A:169 , ARG A:170 , LEU A:195 , HOH A:401 , HOH A:414 , HOH A:423 , HOH A:432 , HOH A:445 , HOH A:456 , HOH A:601 , HOH A:674binding site for residue CIT A 302
03AC3SOFTWAREGLY A:66 , GLN A:67 , ASP A:68 , TYR A:70 , SER A:80 , PHE A:81 , SER A:93 , ASN A:127 , HIS A:191 , CIT A:301 , HOH A:571 , HOH A:705binding site for residue 6UA A 303
04AC4SOFTWAREGLY A:39 , ARG A:41 , GLY A:203 , SER A:204 , ARG A:205 , ARG A:209 , HOH A:473binding site for residue DMS A 304
05AC5SOFTWAREILE A:36 , ARG A:41 , TYR A:42 , GLU A:212 , HOH A:643binding site for residue DMS A 305
06AC6SOFTWARETHR A:54 , PHE A:55 , HOH A:497 , HOH A:728binding site for residue DMS A 306
07AC7SOFTWAREPRO A:89 , TRP A:90 , ALA A:95 , HOH A:611 , HOH A:623 , HOH A:638binding site for residue DMS A 307
08AC8SOFTWAREGLU A:8 , LEU A:9 , VAL A:10 , GLU A:11binding site for residue DMS A 308
09AC9SOFTWAREARG A:41 , ARG A:133 , HOH A:477 , HOH A:608binding site for residue CL A 309
10AD1SOFTWAREGLN A:120binding site for residue IPA A 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WS2)

(-) Cis Peptide Bonds  (2, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:43 -Pro A:44
2Arg A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WS2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WS2)

(-) Exons   (0, 0)

(no "Exon" information available for 4WS2)

(-) 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.eeeee........................hhhhhhhhhhhhhhhh........hhhhhhh.eeeee................hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ws2 A   0 SMTARPLSELVERGWAAALEPVADQVAHMGQFLRAEIAAGRRYLPAGSNVLRAFTFPFDNVRVLIVGQDPYPTPGHAVGLSFSVAPDVRPWPRSLANIFDEYTADLGYPLPSNGDLTPWAQRGVLLLNRVLTVRPSNPASHRGKGWEAVTECAIRALAARAAPLVAILWGRDASTLKPMLAAGNCVAIESPHPSPLSASRGFFGSRPFSRANELLVGMGAEPIDWRLP 227
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
   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)

(no "SCOP Domain" information available for 4WS2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WS2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WS2)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        UNG_MYCTU | P9WFQ9: 2zhx 3a7n 4wpk 4wpl 4wru 4wrv 4wrw 4wrx 4wry 4wrz 4ws0 4ws1 4ws3 4ws4 4ws5 4ws6 4ws7 4ws8

(-) Related Entries Specified in the PDB File

4wru 4wrv 4wrw 4wrx 4wry 4wrz 4ws0 4ws1 4ws3 4ws4 4ws5 4ws6 4ws7 4ws8