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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI 5'-METHYLTHIOADENOSINE/S-ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH 2-(2-HYDROXYETHOXY)ETHYLTHIOMETHYL-DADME-IMMUCILLIN-A
 
Authors :  S. A. Cameron, S. Wang, S. C. Almo, V. L. Schramm
Date :  02 Oct 14  (Deposition) - 25 Nov 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C, D
    EC Number: 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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
13QA4Ligand/Ion(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(2-{[2-(2-HYDROXYETHOXY)ETHYL]SULFANYL}ETHYL)PYRROLIDIN-3-OL
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
13QA2Ligand/Ion(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(2-{[2-(2-HYDROXYETHOXY)ETHYL]SULFANYL}ETHYL)PYRROLIDIN-3-OL
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
13QA2Ligand/Ion(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(2-{[2-(2-HYDROXYETHOXY)ETHYL]SULFANYL}ETHYL)PYRROLIDIN-3-OL
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:9 , ILE A:52 , VAL A:78 , ALA A:79 , GLY A:80 , GLN A:152 , PHE A:153 , VAL A:154 , VAL A:172 , GLU A:173 , MET A:174 , GLU A:175 , SER A:197 , ASP A:198 , ALA A:200 , PHE A:208 , HOH A:436 , HOH A:483 , HIS B:109 , PRO B:115binding site for residue 3QA A 301
2AC2SOFTWAREGLU A:210 , HOH A:406 , HOH A:412 , HOH A:421 , SER D:124 , GLY D:125 , SER D:126binding site for residue SO4 A 302
3AC3SOFTWAREPHE A:107 , HIS A:109 , PRO A:115 , ALA B:9 , MET B:10 , ILE B:52 , VAL B:78 , ALA B:79 , GLY B:80 , GLN B:152 , PHE B:153 , VAL B:154 , VAL B:172 , GLU B:173 , MET B:174 , GLU B:175 , SER B:197 , ASP B:198 , ALA B:200 , PHE B:208 , HOH B:403 , HOH B:425 , HOH B:451 , ASN C:136binding site for residue 3QA B 301
4AC4SOFTWAREGLU B:210 , HOH B:419 , HOH B:422 , SER C:124 , GLY C:125 , SER C:126 , PRO C:189binding site for residue SO4 B 302
5AC5SOFTWAREALA C:9 , GLU C:12 , ILE C:52 , VAL C:78 , ALA C:79 , GLY C:80 , PHE C:153 , VAL C:154 , VAL C:172 , GLU C:173 , MET C:174 , GLU C:175 , SER C:197 , ASP C:198 , ALA C:200 , PHE C:208 , HOH C:463 , HOH C:524 , PHE D:107binding site for residue 3QA C 301
6AC6SOFTWAREPHE C:107 , ALA D:9 , GLU D:12 , ILE D:52 , VAL D:78 , ALA D:79 , GLY D:80 , PHE D:153 , VAL D:154 , VAL D:172 , GLU D:173 , MET D:174 , GLU D:175 , SER D:197 , ASP D:198 , ALA D:200 , PHE D:208 , HOH D:443 , HOH D:547binding site for residue 3QA D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WKP)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhh...eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhheeeee.hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wkp A   1 VQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230


Chain B from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhh...eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhheeeee.hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wkp B   1 VQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230


Chain C from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhh...eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhh..eee.hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wkp C   1 VQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230


Chain D from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhh...eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhheeeee.hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wkp D   1 VQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4WKP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric 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 4ynb 4yo8 5ccd 5cce 5jpc 5k1z 5kb3

(-) Related Entries Specified in the PDB File

4ffs 4FFS CONTAINS THE SAME PROTEIN (WITH A DIFFERENT TAG) COMPLEXED WITH BUTYLTHIO-DADME-IMMUCILLIN-A
4wkc
4wkn 4WKN CONTAINS THE SAME PROTEIN COMPLEXED WITH METHYLTHIO-DADME- IMMUCILLIN-A
4wko 4WKO CONTAINS THE SAME PROTEIN COMPLEXED WITH HYDROXYBUTYLTHIO- DADME-IMMUCILLIN-A