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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI 5'-METHYLTHIOADENOSINE/S-ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH (((4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL)(HEXYL)AMINO)METHANOL
 
Authors :  S. A. Cameron, S. Wang, S. C. Almo, V. L. Schramm
Date :  11 Mar 15  (Deposition) - 25 Nov 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Wang, S. A. Cameron, K. Clinch, G. B. Evans, Z. Wu, V. L. Schramm, P. C. Tyler
New Antibiotic Candidates Against Helicobacter Pylori.
J. Am. Chem. Soc. V. 137 14275 2015
PubMed-ID: 26494017  |  Reference-DOI: 10.1021/JACS.5B06110
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINODEOXYFUTALOSINE NUCLEOSIDASE
    Chains: A, B
    EC Number: 3.2.2.30, 3.2.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MTNN, MTN, JHP_0082
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85963
    Strain: J99 / ATCC 700824
    Synonym: AMINOFUTALOSINE NUCLEOSIDASE,5'-METHYLTHIOADENOSINE/S- ADENOSYLHOMOCYSTEINE NUCLEOSIDASE,MTAN,6-AMINO-6-DEOXYFUTALOSINE N- RIBOSYLHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
14EZ2Ligand/Ion{[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL](HEXYL)AMINO}METHANOL
2ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:79 , ALA A:80 , GLY A:81 , PHE A:154 , VAL A:155 , VAL A:173 , GLU A:174 , MET A:175 , GLU A:176 , SER A:198 , ASP A:199 , HOH A:410 , PHE B:108binding site for residue 4EZ A 301
2AC2SOFTWAREGLU A:211binding site for residue ZN A 302
3AC3SOFTWAREPHE A:108 , VAL B:79 , ALA B:80 , GLY B:81 , PHE B:154 , VAL B:155 , GLU B:174 , MET B:175 , GLU B:176 , SER B:198 , ASP B:199 , PHE B:209 , HOH B:416binding site for residue 4EZ B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YO8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YO8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YO8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YO8)

(-) Exons   (0, 0)

(no "Exon" information available for 4YO8)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....eeeeeee.hhhhhhhhhhhhh...eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhh..eee.hhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yo8 A  -6 HENLYFQGVQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL 231
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        


Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....eeeeeee.hhhhhhhhhhhhh...eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhheeeee.hhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yo8 B -10 HHHHHENLYFQGVQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL 231
                                    -1         9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229
   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 4YO8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YO8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YO8)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MQMTN_HELPJ | Q9ZMY2: 3nm4 3nm5 3nm6 4ffs 4ojt 4oy3 4p54 4wkn 4wko 4wkp 4ynb 5ccd 5cce 5jpc 5k1z 5kb3

(-) Related Entries Specified in the PDB File

4ffs 4FFS CONTAINS THE SAME PROTEIN COMPLEXED WITH BUTYLTHIO-DADME- IMMUCILLIN-A
4wkn 4WKN CONTAINS THE SAME PROTEIN COMPLEXED WITH METHYLTHIO-DADME- IMMUCILLIN-A
4wko 4WKO CONTAINS THE SAME PROTEIN COMPLEXED WITH HYDROXYBUTYLTHIO- DADME-IMMUCILLIN-A
4wkp 4WKP CONTAINS THE SAME PROTEIN COMPLEXED WITH 2-(2-HYDROXYETHOXY) ETHYLTHIOMETHYL-DADME-IMMUCILLIN-A
4ynb 4YNB CONTAINS THE SAME PROTEIN COMPLEXED WITH PYRAZINYLTHIO-DADME- IMMUCILLIN-A