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(-) Description

Title :  CRYSTAL STRUCTURE OF TEHB-LIKE SAM-DEPENDENT METHYLTRANSFERASE (NP_600671.1) FROM CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  05 Mar 08  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Np_600671. 1, Tehb-Like Sam-Dependent Methyltransferase, Methyltransferase Domain, 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 Tehb-Like Sam-Dependent Methyltransferase (Np_600671. 1) From Corynebacterium Glutamicum Atcc 13032 Kitasato At 2. 00 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SAM-DEPENDENT METHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_600671.1, CG1645
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM ATCC 13032
    Organism Taxid: 196627
    Strain: DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO8Ligand/Ion1,2-ETHANEDIOL
3MSE4Mod. Amino AcidSELENOMETHIONINE
4NHE2Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1CIT-1Ligand/IonCITRIC ACID
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MSE2Mod. Amino AcidSELENOMETHIONINE
4NHE2Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MSE2Mod. Amino AcidSELENOMETHIONINE
4NHE-1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:53 , ASP A:74 , LEU A:75 , GLY A:95 , ASP A:96 , LEU A:97 , SER A:112 , ARG B:21BINDING SITE FOR RESIDUE NHE A 195
02AC2SOFTWAREALA A:19 , TRP A:22 , GLY A:155 , LEU A:158BINDING SITE FOR RESIDUE NHE A 196
03AC3SOFTWAREASP A:9 , TYR B:33 , LYS B:65 , ASP B:86BINDING SITE FOR RESIDUE CIT B 195
04AC4SOFTWARELEU A:120 , ARG B:21BINDING SITE FOR RESIDUE EDO A 197
05AC5SOFTWARETHR A:73 , ASP A:100 , GLN A:101BINDING SITE FOR RESIDUE EDO A 198
06AC6SOFTWARESER B:98 , PRO B:127 , ARG B:134BINDING SITE FOR RESIDUE EDO B 196
07AC7SOFTWARETYR A:62 , GLN A:66 , TYR B:62 , GLN B:66BINDING SITE FOR RESIDUE EDO A 199
08AC8SOFTWAREILE A:102 , SER A:103 , GLU A:104 , SER B:103BINDING SITE FOR RESIDUE EDO A 200
09AC9SOFTWARELYS A:178 , ASP B:108 , LEU B:109 , ASP B:139 , ARG B:141BINDING SITE FOR RESIDUE EDO B 197
10BC1SOFTWARETYR A:33 , TYR A:62 , LYS A:65 , PHE A:87BINDING SITE FOR RESIDUE EDO A 201
11BC2SOFTWARESER A:103 , GLN B:101 , ILE B:102 , SER B:103 , GLU B:104BINDING SITE FOR RESIDUE EDO B 198

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CGG)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn B:11 -Pro B:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CGG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CGG)

(-) Exons   (0, 0)

(no "Exon" information available for 3CGG)

(-) 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:186
 aligned with Q8NQI0_CORGL | Q8NQI0 from UniProtKB/TrEMBL  Length:225

    Alignment length:186
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219      
         Q8NQI0_CORGL    40 DNNPAHSENYAQRWRNLAAAGNDIYGEARLIDAMAPRGAKILDAGCGQGRIGGYLSKQGHDVLGTDLDPILIDYAKQDFPEARWVVGDLSVDQISETDFDLIVSAGNVMGFLAEDGREPALANIHRALGADGRAVIGFGAGRGWVFGDFLEVAERVGLELENAFESWDLKPFVQGSEFLVAVFTKK 225
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3cggA00 A:9-194 Vaccinia Virus protein VP39                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhhhhh...hhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeee............eeeeee...hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee.....hhhhhhhhhhhhheeeeeee.............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cgg A   9 DNNPAHSENYAQRWRNLAAAGNDIYGEARLIDAmAPRGAKILDAGCGQGRIGGYLSKQGHDVLGTDLDPILIDYAKQDFPEARWVVGDLSVDQISETDFDLIVSAGNVmGFLAEDGREPALANIHRALGADGRAVIGFGAGRGWVFGDFLEVAERVGLELENAFESWDLKPFVQGSEFLVAVFTKK 194
                                    18        28        38   |    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      
                                                            42-MSE                                                                    117-MSE                                                                         


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with Q8NQI0_CORGL | Q8NQI0 from UniProtKB/TrEMBL  Length:225

    Alignment length:184
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    
         Q8NQI0_CORGL    42 NPAHSENYAQRWRNLAAAGNDIYGEARLIDAMAPRGAKILDAGCGQGRIGGYLSKQGHDVLGTDLDPILIDYAKQDFPEARWVVGDLSVDQISETDFDLIVSAGNVMGFLAEDGREPALANIHRALGADGRAVIGFGAGRGWVFGDFLEVAERVGLELENAFESWDLKPFVQGSEFLVAVFTKK 225
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cggB00 B:11-194 Vaccinia Virus protein VP39                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeee............eeeeee..hhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee.....hhhhhhhhhhhhheeeeeee.............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cgg B  11 NPAHSENYAQRWRNLAAAGNDIYGEARLIDAmAPRGAKILDAGCGQGRIGGYLSKQGHDVLGTDLDPILIDYAKQDFPEARWVVGDLSVDQISETDFDLIVSAGNVmGFLAEDGREPALANIHRALGADGRAVIGFGAGRGWVFGDFLEVAERVGLELENAFESWDLKPFVQGSEFLVAVFTKK 194
                                    20        30        40 |      50        60        70        80        90       100       110      |120       130       140       150       160       170       180       190    
                                                          42-MSE                                                                    117-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3CGG)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CGG)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8NQI0_CORGL | Q8NQI0)
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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