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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS MUTT1 IN COMPLEX WITH PHOSPHATE AND MAGNESIUM IONS (EXCESS MAGNESIUM, 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 :  1.85
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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MG6Ligand/IonMAGNESIUM ION
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:65 , GLY A:66 , LYS A:67 , GLU A:81 , GLU A:85 , GLU A:127 , MG A:402 , MG A:403 , MG A:404 , HOH A:570 , HOH A:584 , HOH A:650 , HOH A:676binding site for residue PO4 A 401
2AC2SOFTWARELYS A:65 , GLU A:85 , GLU A:127 , PO4 A:401 , MG A:403 , HOH A:613 , HOH A:650binding site for residue MG A 402
3AC3SOFTWAREGLU A:81 , GLU A:85 , GLU A:127 , PO4 A:401 , MG A:402 , MG A:404 , HOH A:584binding site for residue MG A 403
4AC4SOFTWAREGLU A:81 , PO4 A:401 , MG A:403 , HOH A:501 , HOH A:603 , HOH A:676binding site for residue MG A 404
5AC5SOFTWARELYS B:65 , GLY B:66 , LYS B:67 , GLU B:81 , GLU B:85 , GLU B:127 , MG B:402 , MG B:403 , MG B:404 , HOH B:517 , HOH B:592 , HOH B:669binding site for residue PO4 B 401
6AC6SOFTWARELYS B:65 , GLU B:85 , GLU B:127 , PO4 B:401 , MG B:403 , HOH B:588 , HOH B:592binding site for residue MG B 402
7AC7SOFTWAREGLU B:81 , GLU B:85 , GLU B:127 , PO4 B:401 , MG B:402 , MG B:404 , HOH B:517binding site for residue MG B 403
8AC8SOFTWAREGLU B:81 , PO4 B:401 , MG B:403 , HOH B:534 , HOH B:547 , HOH B:669binding site for residue MG B 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln B:70 -Gly B:71

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GGC)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               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
                 5ggc A  22 HTVRAAGAVLWRDATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDE 321
                                    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         
                                        35|                                                                                                                                                                                                                                                                                  
                                         47                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeee....eee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeeeee..eeeeeeeeeeeeeee.........eeeeehhhhhhhhh.hhhhhhhhhhhhhh....eeeeeee...................hhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh.............eeeeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggc B  22 HTVRAAGAVLWRDATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDE 321
                                    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         
                                        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 5GGC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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        A0QUZ2_MYCS2 | A0QUZ2: 5gg5 5gg6 5gg7 5gg8 5gg9 5gga 5ggb 5ggd

(-) Related Entries Specified in the PDB File

5gg5 5gg6 5gg7 5gg8 5gg9 5gga 5ggb 5ggd