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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLTRANSFERASE FKBM (YP_546752.1) FROM METHYLOBACILLUS FLAGELLATUS KT AT 2.20 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  15 May 07  (Deposition) - 29 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Yp_546752. 1, Methyltransferase Fkbm, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Methyltransferase Fkbm (Yp_546752. 1) From Methylobacillus Flagellatus Kt At 2. 20 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHYLTRANSFERASE FKBM
    Atcc: 51484
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_546752.1, MFLA_2648
    Organism Scientific: METHYLOBACILLUS FLAGELLATUS KT
    Organism Taxid: 265072
    Strain: KT, DSM 6875

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (4, 48)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO16Ligand/Ion1,2-ETHANEDIOL
3MSE24Mod. Amino AcidSELENOMETHIONINE
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5UNL4Ligand/IonUNKNOWN LIGAND

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:40 , ILE A:137 , HIS A:139BINDING SITE FOR RESIDUE CL A 409
2AC2SOFTWAREGLU A:143 , ASP A:160 , ASP A:161 , TRP A:162 , PHE A:195 , HIS A:196 , CYS A:199 , ARG A:400BINDING SITE FOR RESIDUE EDO A 410
3AC3SOFTWAREHIS A:286 , ARG A:325BINDING SITE FOR RESIDUE EDO A 411
4AC4SOFTWAREPRO A:15 , LEU A:16 , ALA A:17 , MSE A:18 , ASN A:19 , VAL A:186 , TYR A:190 , HOH A:493BINDING SITE FOR RESIDUE EDO A 412
5AC5SOFTWAREARG A:168 , THR A:294 , ILE A:295 , ASP A:323 , VAL A:324 , ARG A:325 , HOH A:420 , HOH A:530BINDING SITE FOR RESIDUE EDO A 413
6AC6SOFTWAREGLY A:233 , ILE A:257 , PRO A:259 , GLY A:289 , ALA A:290 , ILE A:342 , GLY A:344BINDING SITE FOR RESIDUE UNL A 414
7AC7SOFTWAREARG A:126 , ILE A:236 , GLY A:237 , GLU A:238 , ALA A:241 , VAL A:270 , ARG A:273 , HOH A:563 , HOH A:619 , HOH A:779BINDING SITE FOR RESIDUE PEG A 415

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PY6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:111 -Asp A:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PY6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PY6)

(-) Exons   (0, 0)

(no "Exon" information available for 2PY6)

(-) 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:375
 aligned with Q1GXX6_METFK | Q1GXX6 from UniProtKB/TrEMBL  Length:408

    Alignment length:395
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403     
         Q1GXX6_METFK    14 DPLAMNDSFLAAADALAVDPMFGIPANVREVIARRGNATRLVILGTKGFGAHLMNVRHERPCEVIAAVDDFRYHSGELYYGLPIISTDRFTELATHDRDLVALNTCRYDGPKRFFDQICRTHGIPHLNFEQAVRAFGLQGNVDYRVDDWGADIVRNIPAFQTLAQRLADDYSVQTLYAVLNFHLTCEPEYYHEVERPYSTLYFRSGLLRFSDSEKMVDCGASIGESLAGLIGVTKGKFERVWMIEPDRINLQTLQNVLRRYTDTNFASRITVHGCGAGENTIRVPFNHEGGHGGFVKPADADHEPADLIDVRPIDDIIDDAPTFIKMDIEGSELSALKGARRAISEHKPKLAISAYHRSTDLLDLTNYILSIRPDYQIGLRHHTPDRWDTCLYFY 408
               SCOP domains d2py6a1 A:14-408 Methyltransferase FkbM                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----------------------2py6A02 A:36-155 NAD(P)-binding Rossmann-like Domain                                                                    -----------------------------------------------------2py6A03 A:209-408 Vaccinia Virus protein VP39                                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Methyltransf_21-2py6A01 A:231-389                                                                                                                              ------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...eeeee....hhhhhhh.......eeeeee.........ee..eeeehhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh...eeehhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhh.............eeeee....hhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhh....hhh.eeee..ee....eee..--------------------..eeeehhhhhh.....eeee....hhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhh...eeeeee.......eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py6 A  14 DPLAmNDSFLAAADALAVDPmFGIPANVREVIARRGNATRLVILGTKGFGAHLmNVRHERPCEVIAAVDDFRYHSGELYYGLPIISTDRFTELATHDRDLVALNTCRYDGPKRFFDQICRTHGIPHLNFEQAVRAFGLQGNVDYRVDDWGADIVRNIPAFQTLAQRLADDYSVQTLYAVLNFHLTCEPEYYHEVERPYSTLYFRSGLLRFSDSEKmVDCGASIGESLAGLIGVTKGKFERVWmIEPDRINLQTLQNVLRRYTDTNFASRITVHGCGAGENTIRVPF--------------------DLIDVRPIDDIIDDAPTFIKmDIEGSELSALKGARRAISEHKPKLAISAYHRSTDLLDLTNYILSIRPDYQIGLRHHTPDRWDTCLYFY 408
                                |   23        33|       43        53        63   |    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     | 233       243       253  |    263       273       283       293     |   -         -      |323       333      |343       353       363       373       383       393       403     
                                |              34-MSE                           67-MSE                                                                                                                                                           229-MSE                    256-MSE                                    299                  320                 340-MSE                                                                
                               18-MSE
   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  (1, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q1GXX6_METFK | Q1GXX6)
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.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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