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(-) Description

Title :  CRYSTAL STRUCTURE OF BCHU COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE AND ZN-BACTERIOPHEOPHORBIDE D
 
Authors :  H. Yamaguchi, K. Wada, K. Fukuyama
Date :  04 Apr 05  (Deposition) - 18 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
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  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO41Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:150 , HIS A:290BINDING SITE FOR RESIDUE ZN A 5001
2AC2SOFTWAREASN A:74 , THR A:83 , GLU A:84BINDING SITE FOR RESIDUE SO4 A 4396
3AC3SOFTWAREGLU A:147 , HIS A:150 , GLY A:177 , GLY A:179 , ILE A:183 , ASN A:200 , LEU A:201 , VAL A:226 , ASP A:227 , ILE A:228 , CYS A:242 , ARG A:243 , HOH A:5019BINDING SITE FOR RESIDUE SAH A 4261
4AC4SOFTWARETHR A:139 , ARG A:140 , HOH A:5018BINDING SITE FOR RESIDUE GOL A 1019

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X1D)

(-) 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 1X1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X1D)

(-) Exons   (0, 0)

(no "Exon" information available for 1X1D)

(-) 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:337
 aligned with Q8KGE0_CHLTE | Q8KGE0 from UniProtKB/TrEMBL  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
         Q8KGE0_CHLTE     2 SNNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAEGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLEDGKWSLTEFADYMFSPTPKEPNLHQTPVAKAMAFLADDFYMGLSQAVRGQKNFKGQVPYPPVTREDNLYFEEIHRSNAKFAIQLLLEEAKLDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNENAAEKGVADRMRGIAVDIYKESYPEADAVLFCRILYSANEQLSTIMCKKAFDAMRSGGRLLILDMVIDDPENPNFDYLSHYILGAGMPFSVLGFKEQARYKEILESLGYKDVTMVRKYDHLLVQAVKP 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------Methyltransf_2-1x1dA01 A:92-297                                                                                                                                                                               ----------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhh.eeee..eeeehhhhhhhh..........hhhhhhhhhhhhhhh..hhhhhhh..............hhhhhhhhhhhhhh.hhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee............eeeee......hhhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhh..........hhhhhhhhhh..eeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x1d A   2 SNNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAEGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLEDGKWSLTEFADYMFSPTPKEPNLHQTPVAKAMAFLADDFYMGLSQAVRGQKNFKGQVPYPPVTREDNLYFEEIHRSNAKFAIQLLLEEAKLDGVKKMIDVGGGIGDISAAMLKHFPELDSTILNLPGAIDLVNENAAEKGVADRMRGIAVDIYKESYPEADAVLFCRILYSANEQLSTIMCKKAFDAMRSGGRLLILDMVIDDPENPNFDYLSHYILGAGMPFSVLGFKEQARYKEILESLGYKDVTMVRKYDHLLVQAVKP 338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
   Legend:   → Mismatch (orange background)
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  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 1X1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X1D)

(-) 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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8KGE0_CHLTE | Q8KGE0: 1x19 1x1a 1x1b 1x1c

(-) Related Entries Specified in the PDB File

1x19 BCHU INVOLVED IN BACTERIOCHLOROPHYLL C BIOSYNTHESIS
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+