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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS MUTT1 IN COMPLEX WITH 8-OXO-DGTP
 
Authors :  S. M. Arif, A. G. Patil, U. Varshney, M. Vijayan
Date :  15 Jun 16  (Deposition) - 19 Apr 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  8-Oxo-Guanine Nucleotides, Sanitization Of Nucleotide Pool, Nudix Enzyme, Histidine Phosphatase Domain, Binding Sites At Intermolecular Interface, Enzyme Action, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Arif, A. G. Patil, U. Varshney, M. Vijayan
Biochemical And Structural Studies Of Mycobacterium Smegmatis Mutt1, A Sanitization Enzyme With Unusual Modes O Association
Acta Crystallogr D Struct V. 73 349 2017 Biol
PubMed-ID: 28375146  |  Reference-DOI: 10.1107/S2059798317002534
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDROLASE, NUDIX FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JW0097
    Expression System Taxid: 562
    Gene: MSMEG_2390
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Strain: MC2 155
    Synonym: MUTT1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
18DG2Ligand/Ion8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2CL5Ligand/IonCHLORIDE ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
18DG1Ligand/Ion8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18DG1Ligand/Ion8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:55 , ARG A:57 , TYR A:58 , LYS A:65 , LYS A:67 , TYR A:101 , LYS A:108 , GLU A:127 , TYR A:145 , ASP A:147 , ASP A:148 , MG A:402 , HOH A:518 , HOH A:526 , HOH A:551 , HOH A:562 , HOH A:564 , HOH A:568 , HOH A:575 , HOH A:582 , HOH A:594 , HOH A:617 , HOH A:686binding site for residue 8DG A 401
02AC2SOFTWARELYS A:65 , GLU A:85 , GLU A:127 , 8DG A:401 , HOH A:555 , HOH A:682binding site for residue MG A 402
03AC3SOFTWAREHIS A:170 , ARG A:186binding site for residue CL A 403
04AC4SOFTWAREHIS A:88 , ASP A:121 , PHE A:122 , TRP A:133 , HOH A:775binding site for residue CL A 404
05AC5SOFTWAREASP A:215 , HIS A:220binding site for residue EDO A 405
06AC6SOFTWAREGLN A:144 , ARG A:149 , HOH A:504 , HOH A:511 , HOH A:662binding site for residue EDO A 406
07AC7SOFTWARETHR A:292 , TYR A:315 , LEU A:316 , SER A:317 , HOH A:593 , HOH A:696binding site for residue EDO A 407
08AC8SOFTWAREARG B:55 , ARG B:57 , TYR B:58 , LYS B:65 , LYS B:67 , TYR B:101 , LYS B:108 , GLU B:127 , TYR B:145 , ASP B:147 , ASP B:148 , MG B:402 , HOH B:531 , HOH B:541 , HOH B:542 , HOH B:549 , HOH B:552 , HOH B:555 , HOH B:563 , HOH B:588 , HOH B:611 , HOH B:616 , HOH B:631 , HOH B:684binding site for residue 8DG B 401
09AC9SOFTWARELYS B:65 , GLU B:85 , GLU B:127 , 8DG B:401 , HOH B:534 , HOH B:695binding site for residue MG B 402
10AD1SOFTWAREARG B:262 , PRO B:263binding site for residue CL B 403
11AD2SOFTWAREHIS B:170 , ARG B:186binding site for residue CL B 404
12AD3SOFTWAREHIS B:88 , ASP B:121 , PHE B:122 , TRP B:133 , HOH B:730binding site for residue CL B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GG6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His B:44 -Pro B:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GG6)

(-) Exons   (0, 0)

(no "Exon" information available for 5GG6)

(-) Sequences/Alignments

Asymmetric 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:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeee....eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeeee..eeeeeeeeeeeeeee.........eeeeeehhhhhhhh.hhhhhhhhhhhhhh....eeeeeee............hhhhh..hhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh............eeeeeee..eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gg6 A  22 HTVRAAGAVLWRDATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK 322
                                    31   ||   52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
                                        35|                                                                                                                                                                                                                                                                                   
                                         47                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.......eeeeeeee....eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeeee..eeeeeeeeeeeeeee.........eeeeehhhhhhhhh.hhhhhhhhhhhhhh....eeeeeee............hhhhh..hhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh............eeeeeee..eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gg6 B  22 HTVRAAGAVLWRDATGHPATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK 322
                                    31   ||   47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317     
                                        35|                                                                                                                                                                                                                                                                                        
                                         42
   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 5GG6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GG6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GG6)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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        A0QUZ2_MYCS2 | A0QUZ2: 5gg5 5gg7 5gg8 5gg9 5gga 5ggb 5ggc 5ggd

(-) Related Entries Specified in the PDB File

5gg5 5gg7 5gg8 5gg9 5gga 5ggb 5ggc 5ggd