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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE SAM-DEPENDENT METHYLTRANSFERASE NGO1261 FROM NEISSERIA GONORRHOEAE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET NGR48
 
Authors :  F. Forouhar, M. Abashidze, J. Seetharaman, L. Mao, C. Nwosu, Y. Fang, R. Xiao, M. C. Baran, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  06 Sep 07  (Deposition) - 25 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, M. Abashidze, J. Seetharaman, L. Mao, C. Nwosu, Y. Fang, R. Xiao, M. C. Baran, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Crystal Structure Of The Sam-Dependent Methyltransferase Ngo1261 From Neisseria Gonorrhoeae.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPF0341 PROTEIN IN RSP 3' REGION
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector: BL21
    Expression System Vector Type: PLASMID
    Gene: NGO1261
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 485
    Strain: MS11, FA 1090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2R6Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R6Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R6Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R6Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R6Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2R6Z)

(-) 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:225
 aligned with RSMJ_NEIGO | P72077 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:251
                                                                                                                                                                                                                                                                                  250  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        |- 
           RSMJ_NEIGO     2 TDILIDDTATEAVRTLIRAFPLVPVSQPPEQGSYLLAEHDTVSLRLVGEKSNVIVDFTSGAAQYRRTKGGGELIAKAVNHTAHPTVWDATAGLGRDSFVLASLGLTVTAFEQHPAVACLLSDGIRRALLNPETQDTAARINLHFGNAAEQMPALVKTQGKPDIVYLDPMYPERRKSAAVKKEMAYFHRLVGEAQDEVVLLHTARQTAKKRVVVKRPRLGEHLAGQAPAYQYTGKSTRFDVYLPYGADKG--   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r6zA01 A:2-55 YhiQ-like domain                       2r6z             A02 A:56-252 Vaccinia Virus protein VP39                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhh....eee.......eeeeee..eeeeee............-------------hhhhhhhhhhhh..eee.....hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh...eeee...-------------hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhh...eeee...eeeeee.....hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6z A   2 TDILIDDTATEAVRTLIRAFPLVPVSQPPEQGSYLLAEHDTVSLRLVGEKSNVIVDFT-------------ELIAKAVNHTAHPTVWDATAGLGRDSFVLASLGLTVTAFEQHPAVACLLSDGIRRALLNPETQDTAARINLHFGNAAEQmPALVKTQGKPDIVYLDPm-------------mAYFHRLVGEAQDEVVLLHTARQTAKKRVVVKRPRLGEHLAGQAPAYQYTGKSTRFDVYLPYGADKGLE 252
                                    11        21        31        41        51       | -         - |      81        91       101       111       121       131       141       151|      161        |-         -  |    191       201       211       221       231       241       251 
                                                                                    59            73                                                                            152-MSE           170-MSE       184-MSE                                                                


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with RSMJ_NEIGO | P72077 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:253
                                                                                                                                                                                                                                                                                  250    
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        |-   
           RSMJ_NEIGO     2 TDILIDDTATEAVRTLIRAFPLVPVSQPPEQGSYLLAEHDTVSLRLVGEKSNVIVDFTSGAAQYRRTKGGGELIAKAVNHTAHPTVWDATAGLGRDSFVLASLGLTVTAFEQHPAVACLLSDGIRRALLNPETQDTAARINLHFGNAAEQMPALVKTQGKPDIVYLDPMYPERRKSAAVKKEMAYFHRLVGEAQDEVVLLHTARQTAKKRVVVKRPRLGEHLAGQAPAYQYTGKSTRFDVYLPYGADKG----   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r6zB01 B:2-55 YhiQ-like domain                       2r6zB02 B:56-254 Vaccinia Virus protein VP39                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhh....eee.......eeeeee..eeeeee............hhhhhhhhh..hhhhhhhhhhhhhh..eee.....hhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh....hhhhhhheeeee.hhhhhhhhhhhhhh...eeee.....-----------hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhh...eeee...eeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6z B   2 TDILIDDTATEAVRTLIRAFPLVPVSQPPEQGSYLLAEHDTVSLRLVGEKSNVIVDFTSGAAQYRRTKGGGELIAKAVNHTAHPTVWDATAGLGRDSFVLASLGLTVTAFEQHPAVACLLSDGIRRALLNPETQDTAARINLHFGNAAEQmPALVKTQGKPDIVYLDPmYP-----------mAYFHRLVGEAQDEVVLLHTARQTAKKRVVVKRPRLGEHLAGQAPAYQYTGKSTRFDVYLPYGADKGLEHH 254
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151|      161       171|        -  |    191       201       211       221       231       241       251   
                                                                                                                                                                                152-MSE           170-MSE       184-MSE                                                                  
                                                                                                                                                                                                    172
   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 2R6Z)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R6Z)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RSMJ_NEIGO | P72077)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008990    rRNA (guanine-N2-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2r6z)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r6z)
 

(-) 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 ](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
  2r6z
    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
  RSMJ_NEIGO | P72077
    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)
  (no 'Enzyme Classificator' available)
    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
  RSMJ_NEIGO | P72077
    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 2R6Z)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2R6Z)