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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS MUTT1 IN COMPLEX WITH 8-OXO-DGTP, 8-OXO-DGMP AND PYROPHOSPHATE (I)
 
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 :  1.70
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, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
18DG2Ligand/Ion8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
28OG2Ligand/Ion8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4POP2Ligand/IonPYROPHOSPHATE 2-
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
18DG1Ligand/Ion8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
28OG1Ligand/Ion8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4POP1Ligand/IonPYROPHOSPHATE 2-
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
18DG1Ligand/Ion8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
28OG1Ligand/Ion8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4POP1Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:55 , TYR A:58 , SER A:62 , LYS A:65 , LYS A:67 , TYR A:101 , LYS A:108 , TYR A:145 , MG A:404 , HOH A:510 , HOH A:515 , HOH A:535 , HOH A:540 , HOH A:573 , HOH A:583 , HOH A:587 , HOH A:616 , HOH A:726binding site for residue 8DG A 401
2AC2SOFTWAREASP A:59 , TRP A:61 , ASP A:141 , GLN A:142 , GLN A:144 , HOH A:532 , HOH A:553 , HOH A:588binding site for residue 8OG A 402
3AC3SOFTWAREARG A:169 , HIS A:170 , ARG A:176 , ARG A:186 , ARG A:218 , GLN A:271 , GLY A:272 , LYS A:297 , HOH A:525 , HOH A:542 , HOH A:560 , HOH A:566 , HOH A:569binding site for residue POP A 403
4AC4SOFTWARELYS A:65 , GLU A:85 , 8DG A:401 , HOH A:585 , HOH A:636 , HOH A:726binding site for residue MG A 404
5AC5SOFTWAREARG B:55 , TYR B:58 , SER B:62 , LYS B:65 , GLY B:66 , LYS B:67 , TYR B:101 , LYS B:108 , TYR B:145 , MG B:404 , HOH B:507 , HOH B:517 , HOH B:528 , HOH B:529 , HOH B:559 , HOH B:594 , HOH B:626 , HOH B:657 , HOH B:669binding site for residue 8DG B 401
6AC6SOFTWAREASP B:59 , TRP B:61 , ASP B:141 , GLN B:142 , GLN B:144 , HOH B:546 , HOH B:567 , HOH B:581 , HOH B:685binding site for residue 8OG B 402
7AC7SOFTWAREARG B:169 , HIS B:170 , ARG B:176 , ARG B:186 , ARG B:218 , GLN B:271 , GLY B:272 , LYS B:297 , HOH B:532 , HOH B:537 , HOH B:538 , HOH B:643binding site for residue POP B 403
8AC8SOFTWARELYS B:65 , GLU B:85 , 8DG B:401 , HOH B:602 , HOH B:628 , HOH B:713binding site for residue MG B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GG7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GG7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GG7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GG7)

(-) Exons   (0, 0)

(no "Exon" information available for 5GG7)

(-) 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:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.....eeeeeee....eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeeee..eeeeeeeeeeeeeee.........eeeeeehhhhhhhh.hhhhhhhhhhhhhh....eeeeeee...................hhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh............eeeeeee..eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gg7 A  22 HTVRAAGAVLWRDAATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK 322
                                    31   ||   51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321 
                                        35|                                                                                                                                                                                                                                                                                    
                                         46                                                                                                                                                                                                                                                                                    


Chain B 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...................hhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh............eeeeeee..eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gg7 B  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
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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 5GG7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GG7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GG7)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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        A0QUZ2_MYCS2 | A0QUZ2: 5gg5 5gg6 5gg8 5gg9 5gga 5ggb 5ggc 5ggd

(-) Related Entries Specified in the PDB File

5gg5 5gg6 5gg8 5gg9 5gga 5ggb 5ggc 5ggd