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(-) Description

Title :  THE X-RAY STRUCTURE OF THE SAM-DEPENDENT UROPORPHYRINOGEN III METHYLTRANSFERASE NIRE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH SAH AND UROPORPHYRINOGEN III
 
Authors :  S. Storbeck, S. Saha, J. Krausze, B. U. Klink, D. W. Heinz, G. Layer
Date :  09 Mar 11  (Deposition) - 01 Jun 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Heme D1 Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Storbeck, S. Saha, J. Krausze, B. U. Klink, D. W. Heinz, G. Layer
Crystal Structure Of The Heme D1 Biosynthesis Enzyme Nire In Complex With Its Substrate Reveals New Insights Into The Catalytic Mechanism Of S- Adenosyl-L-Methionine-Dependent Uroporphyrinogen Iii Methyltransferases.
J. Biol. Chem. V. 286 26754 2011
PubMed-ID: 21632530  |  Reference-DOI: 10.1074/JBC.M111.239855

(-) Compounds

Molecule 1 - METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.107
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A_PRES2-4_NIRE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET32A
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: UROPORPHYRINOGEN III METHYLTRANFERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2UP21Ligand/IonUROPORPHYRINOGEN III
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2UP22Ligand/IonUROPORPHYRINOGEN III

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:27 , LEU A:52 , GLY A:103 , GLY A:104 , ASP A:105 , ILE A:108 , PHE A:109 , THR A:133 , ALA A:134 , CYS A:138 , TYR A:185 , MET A:186 , VAL A:212 , GLN A:214 , GLY A:215 , GLN A:217 , PRO A:242 , THR A:243 , LEU A:244 , UP2 A:1268 , HOH A:2018 , HOH A:2039 , HOH A:2123BINDING SITE FOR RESIDUE SAH A1267
2AC2SOFTWAREASP A:50 , ARG A:51 , LEU A:52 , PHE A:109 , ARG A:111 , ARG A:149 , HIS A:161 , LEU A:162 , GLN A:163 , MET A:186 , LEU A:188 , GLY A:189 , PRO A:241 , SAH A:1267 , HOH A:2042 , HOH A:2123 , HOH A:2124 , HOH A:2125 , HOH A:2126 , HOH A:2128 , HOH A:2129BINDING SITE FOR RESIDUE UP2 A1268

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:241 -Pro A:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YBQ)

(-) 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:242
 aligned with P95417_PSEAI | P95417 from UniProtKB/TrEMBL  Length:279

    Alignment length:254
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262    
         P95417_PSEAI    13 VDFPAGSVALVGAGPGDPGLLTLRAWALLQQAEVVVYDRLVARELIALLPESCQRIYVGKRCGHHSLPQEEINELLVRLARQQRRVVRLKGGDPFIFGRGAEELERLLEAGVDCQVVPGVTAASGCSTYAGIPLTHRDLAQSCTFVTGHLQNDGRLDLDWAGLARGKQTLVFYMGLGNLAEIAARLVEHGLASDTPAALVSQGTQAGQQVTRGALAELPALARRYQLKPPTLIVVGQVVALFAERAMAHPSYLG 266
               SCOP domains d2ybqa_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....hhhhhhhhhhhhhh...eeee....hhhhhh......eeee..--------hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhh...eeee...hhhhhhhhhh............eeeee....----...hhhhhh....eeeee....hhhhhhhhhhhh......eeeeee.......eeeeee..hhhhhhhhh.....eeeee.hhhhhh...eeee..eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ybq A  13 VDFPAGSVALVGAGPGDPGLLTLRAWALLQQAEVVVYDRLVARELIALLPESCQRIYVG--------PQEEINELLVRLARQQRRVVRLKGGDPFIFGRGAEELERLLEAGVDCQVVPGVTAASGCSTYAGIPLTHRDLAQSCTFVTGHLQ----LDLDWAGLARGKQTLVFYMGLGNLAEIAARLVEHGLASDTPAALVSQGTQAGQQVTRGALAELPALARRYQLKPPTLIVVGQVVALFAERAMAHPSYLG 266
                                    22        32        42        52        62        |-       |82        92       102       112       122       132       142       152       162|    | 172       182       192       202       212       222       232       242       252       262    
                                                                                     71       80                                                                                163  168
   Legend:   → Mismatch (orange background)
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  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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YBQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (P95417_PSEAI | P95417)
molecular function
    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.
    GO:0004851    uroporphyrin-III C-methyltransferase activity    Catalysis of the reaction: 2 S-adenosyl-L-methionine + uroporphyrin III = 2 S-adenosyl-L-homocysteine + precorrin-2.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.

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 Related Entries

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        P95417_PSEAI | P95417: 2ybo

(-) Related Entries Specified in the PDB File

2ybo THE X-RAY STRUCTURE OF THE SAM-DEPENDENT UROPORPHYRINOGEN III METHYLTRANSFERASE NIRE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH SAH