Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF BCHU INVOLVED IN BACTERIOCHLOROPHYLL C BIOSYNTHESIS
 
Authors :  H. Yamaguchi, K. Wada, K. Fukuyama
Date :  02 Apr 05  (Deposition) - 18 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Methyltransferase, Bacteriochllochlorophyll, Bchu, Sam, Sah, S- Adenosylmethyonine, S-Adenosylhomocysteine, Ado-Met, Ado-Hcy, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Wada, H. Yamaguchi, J. Harada, K. Niimi, S. Osumi, Y. Saga, H. Oh-Oka H. Tamiaki, K. Fukuyama
Crystal Structures Of Bchu, A Methyltransferase Involved In Bacteriochlorophyll C Biosynthesis, And Its Complex With S-Adenosylhomocysteine: Implications For Reaction Mechanism
J. Mol. Biol. V. 360 839 2006
PubMed-ID: 16797589  |  Reference-DOI: 10.1016/J.JMB.2006.05.057

(-) Compounds

Molecule 1 - CRTF-RELATED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: CHLOROBIUM TEPIDUM
    Organism Taxid: 194439
    Strain: TLS
    Synonym: METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:71 , ASN A:74 , THR A:83 , GLU A:84 , HOH A:4474BINDING SITE FOR RESIDUE SO4 A 4396

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X19)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:135 -Pro A:136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X19)

(-) Exons   (0, 0)

(no "Exon" information available for 1X19)

(-) 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:350
 aligned with Q8KGE0_CHLTE | Q8KGE0 from UniProtKB/TrEMBL  Length:338

    Alignment length:350
                                        1                                                                                                                                                                                                                                                                                                                                                 
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
         Q8KGE0_CHLTE     - ------------MSNNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAEGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLEDGKWSLTEFADYMFSPTPKEPNLHQTPVAKAMAFLADDFYMGLSQAVRGQKNFKGQVPYPPVTREDNLYFEEIHRSNAKFAIQLLLEEAKLDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNENAAEKGVADRMRGIAVDIYKESYPEADAVLFCRILYSANEQLSTIMCKKAFDAMRSGGRLLILDMVIDDPENPNFDYLSHYILGAGMPFSVLGFKEQARYKEILESLGYKDVTMVRKYDHLLVQAVKP 338
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------Methyltransf_2-1x19A01 A:92-297                                                                                                                                                                               ----------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeehhhhhhhh..........hhhhhhhhhhhhhhh..hhhhhhh..............hhhhhhhhhhhhhh.hhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee............eeeee.hhhhhhhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhhh.eeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x19 A -11 HSSGLVPRGSHMMSNNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAEGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLEDGKWSLTEFADYMFSPTPKEPNLHQTPVAKAMAFLADDFYMGLSQAVRGQKNFKGQVPYPPVTREDNLYFEEIHRSNAKFAIQLLLEEAKLDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNENAAEKGVADRMRGIAVDIYKESYPEADAVLFCRILYSANEQLSTIMCKKAFDAMRSGGRLLILDMVIDDPENPNFDYLSHYILGAGMPFSVLGFKEQARYKEILESLGYKDVTMVRKYDHLLVQAVKP 338
                                    -2         8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
   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 1X19)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X19)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8KGE0_CHLTE | Q8KGE0)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:135 - Pro A:136   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  1x19
    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
  Q8KGE0_CHLTE | Q8KGE0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q8KGE0_CHLTE | Q8KGE0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8KGE0_CHLTE | Q8KGE0: 1x1a 1x1b 1x1c 1x1d

(-) Related Entries Specified in the PDB File

1x1a BCHU COMPLEXED WITH S-ADENOSYL-L-METHIONINE
1x1b BCHU COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE
1x1c BCHU COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE AND ZN2+
1x1d BCHU COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE AND ZN- BACTERIOPHEOPHORBIDE D