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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SAM DEPENDENT METHYLTRANSFERASE FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  Y. Kim, A. Joachimiak, X. Xu, J. Gu, A. Edwards, A. Savchenko, Midwest C Structural Genomics (Mcsg)
Date :  25 Sep 06  (Deposition) - 24 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Alpha-Beta Sandwich, Beta-Barrel, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kim, A. Joachimiak, X. Xu, J. Gu, A. Edwards, A. Savchenko
Crystal Structure Of The Sam Dependent Methyltransferase From Agrobacterium Tumefaciens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SAM DEPENDENT METHYLTRANSFERASE
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificAGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid176299
    StrainC58

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)ABC
Biological Unit 2 (2x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 39)

Asymmetric Unit (5, 39)
No.NameCountTypeFull Name
1ACY6Ligand/IonACETIC ACID
2FMT7Ligand/IonFORMIC ACID
3GOL2Ligand/IonGLYCEROL
4MSE21Mod. Amino AcidSELENOMETHIONINE
5SAM3Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (5, 39)
No.NameCountTypeFull Name
1ACY6Ligand/IonACETIC ACID
2FMT7Ligand/IonFORMIC ACID
3GOL2Ligand/IonGLYCEROL
4MSE21Mod. Amino AcidSELENOMETHIONINE
5SAM3Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (5, 78)
No.NameCountTypeFull Name
1ACY12Ligand/IonACETIC ACID
2FMT14Ligand/IonFORMIC ACID
3GOL4Ligand/IonGLYCEROL
4MSE42Mod. Amino AcidSELENOMETHIONINE
5SAM6Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:113 , PHE A:140 , TYR A:142 , ASP A:161 , ALA A:162 , SER A:163 , GLU A:189 , ASP A:190 , ALA A:191 , ASP A:211 , PRO A:213 , GLY A:216 , ARG A:217 , GLY A:218 , TRP A:224 , TYR A:253 , HOH A:1020 , HOH A:1042 , HOH A:1045 , HOH A:1054 , HOH A:1215 , HOH A:1317BINDING SITE FOR RESIDUE SAM A 1001
02AC2SOFTWAREPHE B:113 , PHE B:140 , TYR B:142 , ASP B:161 , ALA B:162 , SER B:163 , GLU B:189 , ASP B:190 , ALA B:191 , ASP B:211 , PRO B:213 , GLY B:216 , ARG B:217 , GLY B:218 , TRP B:224 , TYR B:253 , HOH B:1020 , HOH B:1029 , HOH B:1032 , HOH B:1064 , HOH B:1081 , HOH B:1221 , HOH B:1250 , HOH B:1303BINDING SITE FOR RESIDUE SAM B 1002
03AC3SOFTWAREPHE C:113 , PHE C:140 , TYR C:142 , ASP C:161 , ALA C:162 , SER C:163 , GLU C:189 , ASP C:190 , ALA C:191 , ASP C:211 , PRO C:213 , GLY C:216 , ARG C:217 , GLY C:218 , TRP C:224 , HOH C:1020 , HOH C:1027 , HOH C:1028 , HOH C:1127 , HOH C:1132 , HOH C:1200 , HOH C:1244 , HOH C:1261BINDING SITE FOR RESIDUE SAM C 1003
04AC4SOFTWARELYS A:244 , HOH A:1231 , ARG B:81 , PHE B:82 , PRO B:83 , MSE C:1 , GLN C:196 , GLU C:199 , ASP C:235 , HOH C:1159BINDING SITE FOR RESIDUE GOL C 1004
05AC5SOFTWAREGLU A:189 , PHE A:194 , ARG A:197 , ARG A:201BINDING SITE FOR RESIDUE GOL A 1005
06AC6SOFTWARESER C:242 , HOH C:1339BINDING SITE FOR RESIDUE ACY C 1006
07AC7SOFTWAREARG C:42 , ARG C:59 , ASN C:63 , LEU C:289BINDING SITE FOR RESIDUE ACY C 1007
08AC8SOFTWARESER A:163 , LYS A:164 , LYS A:165 , HOH A:1126BINDING SITE FOR RESIDUE ACY A 1008
09AC9SOFTWARELYS A:164 , ILE A:167 , GLY A:168 , LYS A:171 , HOH A:1172BINDING SITE FOR RESIDUE ACY A 1009
10BC1SOFTWARELEU A:16 , ARG A:305 , HOH A:1100BINDING SITE FOR RESIDUE ACY A 1010
11BC2SOFTWAREGLU C:189 , PHE C:194 , ARG C:197 , ARG C:201BINDING SITE FOR RESIDUE ACY C 1011
12BC3SOFTWAREARG A:79 , MSE B:192 , LYS B:193 , HOH B:1022 , HOH B:1041 , HOH B:1063BINDING SITE FOR RESIDUE FMT B 1012
13BC4SOFTWAREARG A:45 , HIS A:109 , VAL A:110 , GLY A:111 , VAL A:112 , PHE A:113 , TYR A:142 , HOH A:1081 , HOH A:1195BINDING SITE FOR RESIDUE FMT A 1013
14BC5SOFTWAREARG B:45 , HIS B:109 , VAL B:110 , GLY B:111 , VAL B:112 , TYR B:142 , HOH B:1085 , HOH B:1215BINDING SITE FOR RESIDUE FMT B 1014
15BC6SOFTWARESER B:163 , LYS B:164 , LYS B:165BINDING SITE FOR RESIDUE FMT B 1015
16BC7SOFTWAREARG C:45 , HIS C:109 , VAL C:110 , GLY C:111 , VAL C:112 , PHE C:113 , TYR C:142 , HOH C:1250BINDING SITE FOR RESIDUE FMT C 1016
17BC8SOFTWARESER C:163 , LYS C:164 , LYS C:165BINDING SITE FOR RESIDUE FMT C 1017
18BC9SOFTWAREARG B:79 , MSE C:192 , LYS C:193 , HOH C:1031 , HOH C:1041 , HOH C:1048BINDING SITE FOR RESIDUE FMT C 1018

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Val A:12 -Pro A:13
2Val B:12 -Pro B:13
3Val C:12 -Pro C:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IGT)

(-) 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:313
 aligned with A9CKD6_AGRFC | A9CKD6 from UniProtKB/TrEMBL  Length:309

    Alignment length:316
                                   1                                                                                                                                                                                                                                                                                                                    
                                   | 3        13        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      
         A9CKD6_AGRFC     - -------MQRTGELPAEHVPVILESSGAGDFHLIDSGNGLKLEQYGDYRVVRPEAQALWRPLVPDRVWQNADAIFTGDTDEDGMGRWRFPKEALGETWPLSLLGVEFLGRFTAFRHVGVFPEQIVHWEWLKNAVETADRPLKVLNLFGYTGVASLVAAAAGAEVTHVDASKKAIGWAKENQVLAGLEQAPIRWICEDAMKFIQREERRGSTYDIILTDPPKFGRGTHGEVWQLFDHLPLMLDICREILSPKALGLVLTAYSIRASFYSMHELMRETMRGAGGVVASGELVIREAGLDGKTPGRVLSTSLFSRWEPK 309
               SCOP domains -------d2igta1 A:1-309 Putative methyltransferase Atu0340                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2igtA01 A:-6-20,A:89-309   2igtA02 A:21-88 Golgi alpha-mannosidase II                          2igtA01 A:-6-20,A:89-309 Vaccinia Virus protein VP39                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeee.....eeeeeee..eeeeee..eeeeee..........hhhhhhh..eeeee..---..eeee........eeeeee..eeeeee.........hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhh....eeee....eee.....eeehhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhh.....eeeeeeeeee...........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2igt A  -6 ENLYFQGmQRTGELPAEHVPVILESSGAGDFHLIDSGNGLKLEQYGDYRVVRPEAQALWRPLVPDRVWQNADAIFTGDT---GmGRWRFPKEALGETWPLSLLGVEFLGRFTAFRHVGVFPEQIVHWEWLKNAVETADRPLKVLNLFGYTGVASLVAAAAGAEVTHVDASKKAIGWAKENQVLAGLEQAPIRWICEDAmKFIQREERRGSTYDIILTDPPKFGRGTHGEVWQLFDHLPLmLDICREILSPKALGLVLTAYSIRASFYSmHELmRETmRGAGGVVASGELVIREAGLDGKTPGRVLSTSLFSRWEPK 309
                                   | 3        13        23        33        43        53        63        |-  ||    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  |   |273       283       293       303      
                                   1-MSE                                                                 72  76|                                                                                                                192-MSE                                  233-MSE                      262-MSE   |                                       
                                                                                                              77-MSE                                                                                                                                                                                      266-MSE                                       
                                                                                                                                                                                                                                                                                                              270-MSE                                   

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with A9CKD6_AGRFC | A9CKD6 from UniProtKB/TrEMBL  Length:309

    Alignment length:316
                                   1                                                                                                                                                                                                                                                                                                                    
                                   | 3        13        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      
         A9CKD6_AGRFC     - -------MQRTGELPAEHVPVILESSGAGDFHLIDSGNGLKLEQYGDYRVVRPEAQALWRPLVPDRVWQNADAIFTGDTDEDGMGRWRFPKEALGETWPLSLLGVEFLGRFTAFRHVGVFPEQIVHWEWLKNAVETADRPLKVLNLFGYTGVASLVAAAAGAEVTHVDASKKAIGWAKENQVLAGLEQAPIRWICEDAMKFIQREERRGSTYDIILTDPPKFGRGTHGEVWQLFDHLPLMLDICREILSPKALGLVLTAYSIRASFYSMHELMRETMRGAGGVVASGELVIREAGLDGKTPGRVLSTSLFSRWEPK 309
               SCOP domains d2igtb_ B: Putative methyltransferase Atu0340                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2igtB01 B:-6-20,B:89-309   2igtB02 B:21-88 Golgi alpha-mannosidase II                          2igtB01 B:-6-20,B:89-309 Vaccinia Virus protein VP39                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeee.....eeeeeee..eeeeee..eeeeee..........hhhhhhh..eeeee.----..eeee........eeeeee..eeeeee.........hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhh....eeee....eee.....eeehhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhh.....eeeeeeeeee...........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2igt B  -6 ENLYFQGmQRTGELPAEHVPVILESSGAGDFHLIDSGNGLKLEQYGDYRVVRPEAQALWRPLVPDRVWQNADAIFTGD----GmGRWRFPKEALGETWPLSLLGVEFLGRFTAFRHVGVFPEQIVHWEWLKNAVETADRPLKVLNLFGYTGVASLVAAAAGAEVTHVDASKKAIGWAKENQVLAGLEQAPIRWICEDAmKFIQREERRGSTYDIILTDPPKFGRGTHGEVWQLFDHLPLmLDICREILSPKALGLVLTAYSIRASFYSmHELmRETmRGAGGVVASGELVIREAGLDGKTPGRVLSTSLFSRWEPK 309
                                   | 3        13        23        33        43        53        63       | -  ||    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  |   |273       283       293       303      
                                   1-MSE                                                                71   76|                                                                                                                192-MSE                                  233-MSE                      262-MSE   |                                       
                                                                                                              77-MSE                                                                                                                                                                                      266-MSE                                       
                                                                                                                                                                                                                                                                                                              270-MSE                                   

Chain C from PDB  Type:PROTEIN  Length:313
 aligned with A9CKD6_AGRFC | A9CKD6 from UniProtKB/TrEMBL  Length:309

    Alignment length:316
                                   1                                                                                                                                                                                                                                                                                                                    
                                   | 3        13        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      
         A9CKD6_AGRFC     - -------MQRTGELPAEHVPVILESSGAGDFHLIDSGNGLKLEQYGDYRVVRPEAQALWRPLVPDRVWQNADAIFTGDTDEDGMGRWRFPKEALGETWPLSLLGVEFLGRFTAFRHVGVFPEQIVHWEWLKNAVETADRPLKVLNLFGYTGVASLVAAAAGAEVTHVDASKKAIGWAKENQVLAGLEQAPIRWICEDAMKFIQREERRGSTYDIILTDPPKFGRGTHGEVWQLFDHLPLMLDICREILSPKALGLVLTAYSIRASFYSMHELMRETMRGAGGVVASGELVIREAGLDGKTPGRVLSTSLFSRWEPK 309
               SCOP domains d2igtc_ C: Putative methyltransferase Atu0340                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2igtC01 C:-6-20,C:89-309   2igtC02 C:21-88 Golgi alpha-mannosidase II                          2igtC01 C:-6-20,C:89-309 Vaccinia Virus protein VP39                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeee.....eeeeeee..eeeeee..eeeeee..........hhhhhh...eeee..---....eee........eeeeee..eeeeee.........hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhh....eeee....eee.....eeehhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhh.....eeeeeeeeee...........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2igt C  -6 ENLYFQGmQRTGELPAEHVPVILESSGAGDFHLIDSGNGLKLEQYGDYRVVRPEAQALWRPLVPDRVWQNADAIFTGD---DGmGRWRFPKEALGETWPLSLLGVEFLGRFTAFRHVGVFPEQIVHWEWLKNAVETADRPLKVLNLFGYTGVASLVAAAAGAEVTHVDASKKAIGWAKENQVLAGLEQAPIRWICEDAmKFIQREERRGSTYDIILTDPPKFGRGTHGEVWQLFDHLPLmLDICREILSPKALGLVLTAYSIRASFYSmHELmRETmRGAGGVVASGELVIREAGLDGKTPGRVLSTSLFSRWEPK 309
                                   | 3        13        23        33        43        53        63       | - | |    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  |   |273       283       293       303      
                                   1-MSE                                                                71  75 |                                                                                                                192-MSE                                  233-MSE                      262-MSE   |                                       
                                                                                                              77-MSE                                                                                                                                                                                      266-MSE                                       
                                                                                                                                                                                                                                                                                                              270-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, 3)

Asymmetric Unit

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (A9CKD6_AGRFC | A9CKD6)
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: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.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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