Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF VIBRIO CHOLERAE 5'-METHYLTHIOADENOSINE/S-ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH BUTYLTHIO-DADME-IMMUCILLIN A
 
Authors :  M. Ho, J. A. Gutierrez, T. Crowder, A. Rinaldo-Matthis, S. C. Almo, V. L.
Date :  07 Jul 08  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Vibrio Cholerae 5'-Methylthioadenosine/S-Adenosyl Homocysteine Nucleosidase, Butylthio Dadme Immucillin A, Mtan, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Gutierrez, T. Crowder, A. Rinaldo-Matthis, M. C. Ho, S. C. Almo, V. L. Schramm
Transition State Analogs Of 5'-Methylthioadenosine Nucleosidase Disrupt Quorum Sensing.
Nat. Chem. Biol. V. 5 251 2009
PubMed-ID: 19270684  |  Reference-DOI: 10.1038/NCHEMBIO.153

(-) Compounds

Molecule 1 - MTA/SAH NUCLEOSIDASE
    Chains: A, C
    EC Number: 3.2.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD-DEST49
    Expression System Strain: BL21 STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1BIG2Ligand/Ion(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(BUTYLSULFANYL)METHYL]PYRROLIDIN-3-OL
2IOD1Ligand/IonIODIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:139 , PRO C:137 , THR C:139BINDING SITE FOR RESIDUE IOD C 300
2AC2SOFTWAREILE A:50 , SER A:76 , ALA A:77 , GLY A:78 , ALA A:151 , PHE A:152 , VAL A:153 , VAL A:172 , GLU A:173 , MET A:174 , GLU A:175 , SER A:197 , ASP A:198 , PHE A:208 , HOH A:305 , PHE C:105BINDING SITE FOR RESIDUE BIG A 301
3AC3SOFTWAREILE C:50 , SER C:76 , ALA C:77 , GLY C:78 , ALA C:151 , PHE C:152 , VAL C:153 , VAL C:172 , GLU C:173 , MET C:174 , GLU C:175 , SER C:197 , ASP C:198 , PHE C:208 , HOH C:302BINDING SITE FOR RESIDUE BIG C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DP9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DP9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DP9)

(-) Exons   (0, 0)

(no "Exon" information available for 3DP9)

(-) 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:229
 aligned with MTNN_VIBCH | Q9KPI8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:229
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         
           MTNN_VIBCH     2 KIGIIGAMQQEVAILKDLIEDVQEVNQAGCTFYSGQIQGVDVVLLQSGIGKVSAALGTALLISQYAPDVVINTGSAGGFDASLNVGDVVISSEVRHHDADVTAFGYEIGQMAGQPAAFKADEKLMTVAEQALAQLPNTHAVRGLICTGDAFVCTAERQQFIRQHFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESPLSFEEFLPLAAKSSSAMVLKMVELL 230
               SCOP domains d3dp9a_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains 3dp9A00 A:2-230  [code=3.40.50.1580, no name defined]                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhh..eeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhh......eeeeeeee......hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp9 A   2 KIGIIGAMQQEVAILKDLIEDVQEVNQAGCTFYSGQIQGVDVVLLQSGIGKVSAALGTALLISQYAPDVVINTGSAGGFDASLNVGDVVISSEVRHHDADVTAFGYEIGQMAGQPAAFKADEKLMTVAEQALAQLPNTHAVRGLICTGDAFVCTAERQQFIRQHFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESPLSFEEFLPLAAKSSSAMVLKMVELL 230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         


Chain C from PDB  Type:PROTEIN  Length:230
 aligned with MTNN_VIBCH | Q9KPI8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
           MTNN_VIBCH     1 MKIGIIGAMQQEVAILKDLIEDVQEVNQAGCTFYSGQIQGVDVVLLQSGIGKVSAALGTALLISQYAPDVVINTGSAGGFDASLNVGDVVISSEVRHHDADVTAFGYEIGQMAGQPAAFKADEKLMTVAEQALAQLPNTHAVRGLICTGDAFVCTAERQQFIRQHFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESPLSFEEFLPLAAKSSSAMVLKMVELL 230
               SCOP domains d3dp9c_ C: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 3dp9C00 C:1-230  [code=3.40.50.1580, no name defined]                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhh..eeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhhh......eeeeeeee......hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp9 C   1 MKIGIIGAMQQEVAILKDLIEDVQEVNQAGCTFYSGQIQGVDVVLLQSGIGKVSAALGTALLISQYAPDVVINTGSAGGFDASLNVGDVVISSEVRHHDADVTAFGYEIGQMAGQPAAFKADEKLMTVAEQALAQLPNTHAVRGLICTGDAFVCTAERQQFIRQHFPSVVAVEMEASAIAQTCHQFKVPFVVVRAISDVADKESPLSFEEFLPLAAKSSSAMVLKMVELL 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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DP9)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (MTNN_VIBCH | Q9KPI8)
molecular function
    GO:0008782    adenosylhomocysteine nucleosidase activity    Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenine + S-D-ribosyl-L-homocysteine.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008930    methylthioadenosine nucleosidase activity    Catalysis of the reaction: methylthioadenosine + H2O = adenine + 5-methylthio-D-ribose.
biological process
    GO:0019284    L-methionine salvage from S-adenosylmethionine    The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
    GO:0019509    L-methionine salvage from methylthioadenosine    The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    GO:0009164    nucleoside catabolic process    The chemical reactions and pathways resulting in the breakdown of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BIG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dp9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3dp9
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MTNN_VIBCH | Q9KPI8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.2.9
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MTNN_VIBCH | Q9KPI8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3DP9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DP9)