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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE O-METHYLTRANSFERASE FROM BACILLUS HALODURANS
 
Authors :  U. A. Ramagopal, Patskovsky Y. V. , S. C. Almo, S. K. Burley, New York S Research Center For Structural Genomics (Nysgxrc)
Date :  18 Apr 06  (Deposition) - 06 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, Patskovsky Y. V. , S. C. Almo
Crystal Structure Of Putative O-Methyltransferase From Bacillus Halodurans
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - O-METHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 272558
    Strain: C-125

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE14Mod. Amino AcidSELENOMETHIONINE
3ZN9Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN B:160 , ASP B:206 , HOH B:319 , HOH B:371 , HOH B:373 , HOH B:416BINDING SITE FOR RESIDUE MG B 301
02AC2SOFTWAREASP B:206 , GLU B:226 , HIS B:230 , HIS B:233BINDING SITE FOR RESIDUE ZN B 302
03AC3SOFTWAREHIS A:10 , HIS B:31 , HIS B:229BINDING SITE FOR RESIDUE ZN B 303
04AC4SOFTWAREGLU A:29 , GLU A:93 , HIS A:97 , HOH A:373BINDING SITE FOR RESIDUE ZN A 304
05AC5SOFTWAREGLU B:88 , ASP B:144 , HIS B:194 , HOH B:394BINDING SITE FOR RESIDUE ZN B 305
06AC6SOFTWAREGLN A:116 , HOH A:319BINDING SITE FOR RESIDUE ZN A 306
07AC7SOFTWAREGLU B:215BINDING SITE FOR RESIDUE ZN A 307
08AC8SOFTWAREASP A:206BINDING SITE FOR RESIDUE ZN A 308
09AC9SOFTWAREGLU B:29 , GLU B:93 , HIS B:97BINDING SITE FOR RESIDUE ZN B 309
10BC1SOFTWAREASP A:198 , HIS B:48 , LYS B:51BINDING SITE FOR RESIDUE ZN B 310

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:111 -Gly A:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GPY)

(-) 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:185
 aligned with Q9KDE1_BACHD | Q9KDE1 from UniProtKB/TrEMBL  Length:223

    Alignment length:210
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
         Q9KDE1_BACHD     3 EERLKHYLEKQIPARDQYIEQMEREAHEQQVPIMDLLGMESLLHLLKMAAPARILEIGTAIGYSAIRMAQALPEATIVSIERDERRYEEAHKHVKALGLESRIELLFGDALQLGEKLELYPLFDVLFIDAAKGQYRRFFDMYSPMVRPGGLILSDNVLFRGLVAETDIEHKRHKQLATKIDTYNQWLLEHPQYDTRIFPVGDGIAISIKR 212
               SCOP domains d2gpya_ A: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh.....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.....eeee..hhhhhhhhhh....eeeeeee.hhhhhhhhhhhhh..eeeeeeeeee....-------------------------........eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gpy A   5 EERLKHYLEKQIPARDQYIEQmEREAHEQQVPImDLLGmESLLHLLKmAAPARILEIGTAIGYSAIRmAQALPEATIVSIERDERRYEEAHKHVKALGLESRIELLFGDALQLGEKLELYPLFDVLFIDAAKGQYRRFFDmYSPmVRPGGLILSDNVLF-------------------------QWLLEHPQYDTRIFPVGDGIAISIKR 214
                                    14        24 |      34   |    44       |54        64       |74        84        94       104       114       124       134       144|   |  154        |-         -         -    |  194       204       214
                                                26-MSE      38-MSE|       52-MSE              72-MSE                                                                  145-MSE           163                       189                         
                                                                 43-MSE                                                                                                   149-MSE                                                             


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with Q9KDE1_BACHD | Q9KDE1 from UniProtKB/TrEMBL  Length:223

    Alignment length:217
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       
         Q9KDE1_BACHD     6 LKHYLEKQIPARDQYIEQMEREAHEQQVPIMDLLGMESLLHLLKMAAPARILEIGTAIGYSAIRMAQALPEATIVSIERDERRYEEAHKHVKALGLESRIELLFGDALQLGEKLELYPLFDVLFIDAAKGQYRRFFDMYSPMVRPGGLILSDNVLFRGLVAETDIEHKRHKQLATKIDTYNQWLLEHPQYDTRIFPVGDGIAISIKRETKGDTDDEK 222
               SCOP domains d2gpyb_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhh...eeeeeee....hhhhhhhhhh..eeeeeeeeee....------------------------hhhhhhh..eeeeee.....eeeeee..-.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gpy B   8 LKHYLEKQIPARDQYIEQmEREAHEQQVPImDLLGmESLLHLLKmAAPARILEIGTAIGYSAIRmAQALPEATIVSIERDERRYEEAHKHVKALGLESRIELLFGDALQLGEKLELYPLFDVLFIDAAKGQYRRFFDmYSPmVRPGGLILSDNVLF------------------------NQWLLEHPQYDTRIFPVGDGIAISIKRE-EGHHHHHH 233
                                    17        27        37|    |  47    |   57        67    |   77        87        97       107       117       127       137       147 |     157     |   -         -         -|      197       207       226       
                                             26-MSE      38-MSE|       52-MSE              72-MSE                                                                  145-MSE           163                      188                        215 |       
                                                              43-MSE                                                                                                   149-MSE                                                             226
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9KDE1_BACHD | Q9KDE1)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    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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    Phe A:111 - Gly A:112   [ RasMol ]  
 

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