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(-) Description

Title :  CRYSTAL STRUCTURE OF A METHYLTRANSFERASE (NP_951602.1) FROM GEOBACTER SULFURREDUCENS AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  28 Jan 08  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Np_951602. 1, O-Methyltransferase, 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 A Methyltransferase (Np_951602. 1) From Geobacter Sulfurreducens At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHYLTRANSFERASE
    Atcc51573
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidSPEEDET
    Expression System StrainHK100
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneNP_951602.1, GSU0544
    Organism ScientificGEOBACTER SULFURREDUCENS PCA
    Organism Taxid243231
    StrainPCA / DSM 12127

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 51)

Asymmetric Unit (4, 51)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO24Ligand/Ion1,2-ETHANEDIOL
3MSE16Mod. Amino AcidSELENOMETHIONINE
4PEG9Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 30)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO11Ligand/Ion1,2-ETHANEDIOL
3MSE11Mod. Amino AcidSELENOMETHIONINE
4PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 38)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO26Ligand/Ion1,2-ETHANEDIOL
3MSE10Mod. Amino AcidSELENOMETHIONINE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:41 , ARG A:45BINDING SITE FOR RESIDUE CL A 210
02AC2SOFTWAREARG A:189 , GLN B:123BINDING SITE FOR RESIDUE CL B 210
03AC3SOFTWAREGLN A:57 , LEU A:58 , ARG A:124 , HOH A:239BINDING SITE FOR RESIDUE EDO A 212
04AC4SOFTWAREVAL A:5 , ASP A:6 , SER A:7 , GLY A:10 , HOH A:229BINDING SITE FOR RESIDUE EDO A 213
05AC5SOFTWARELEU A:16 , LEU A:17 , PRO A:18 , ARG A:45 , SER B:186 , THR B:193BINDING SITE FOR RESIDUE EDO A 214
06AC6SOFTWAREGLY A:63 , ASP A:87 , ASN A:92BINDING SITE FOR RESIDUE EDO A 215
07AC7SOFTWAREASP A:89 , ASP A:91BINDING SITE FOR RESIDUE EDO A 216
08AC8SOFTWAREASP A:134 , ASN A:159 , ALA A:160 , ARG A:179BINDING SITE FOR RESIDUE EDO A 217
09AC9SOFTWAREPHE A:191 , PHE A:192 , HOH A:241 , ARG B:45 , PEG B:216BINDING SITE FOR RESIDUE EDO A 218
10BC1SOFTWAREVAL B:23 , MSE B:27 , ILE B:30 , HIS B:95 , MSE B:99 , HOH B:252BINDING SITE FOR RESIDUE EDO B 211
11BC2SOFTWAREARG A:52 , GLN A:55 , HOH A:250 , LYS B:54 , ASN B:152 , TYR B:206BINDING SITE FOR RESIDUE EDO B 212
12BC3SOFTWAREALA B:139 , LEU B:142 , GLU B:143 , ARG B:188BINDING SITE FOR RESIDUE EDO B 213
13BC4SOFTWARELYS C:54 , GLN C:55 , PRO C:56 , ASP C:127 , HOH C:269BINDING SITE FOR RESIDUE EDO C 210
14BC5SOFTWAREPRO C:37 , GLY C:65 , ASN C:92 , HOH C:288BINDING SITE FOR RESIDUE EDO C 211
15BC6SOFTWAREASP C:115 , ILE C:119 , EDO C:213BINDING SITE FOR RESIDUE EDO C 212
16BC7SOFTWAREASP C:115 , GLY C:118 , ARG C:144 , EDO C:212 , HOH C:275BINDING SITE FOR RESIDUE EDO C 213
17BC8SOFTWAREASP C:134 , ASN C:159 , LEU C:161 , ARG C:162 , ARG C:163 , ARG C:179BINDING SITE FOR RESIDUE EDO C 214
18BC9SOFTWAREPRO C:37 , ILE C:38 , VAL C:39 , ASP C:132 , ASN C:159 , GLY C:164BINDING SITE FOR RESIDUE EDO C 215
19CC1SOFTWARETYR C:48 , ARG C:75BINDING SITE FOR RESIDUE EDO C 216
20CC2SOFTWAREPRO C:18 , ARG C:45 , PHE C:191 , PHE C:192 , HOH C:225BINDING SITE FOR RESIDUE EDO C 217
21CC3SOFTWAREALA C:20 , ASP C:21 , VAL C:24 , ARG C:41 , ARG C:45BINDING SITE FOR RESIDUE EDO C 218
22CC4SOFTWAREASP C:125 , ARG C:147 , CYS C:148 , LEU C:149BINDING SITE FOR RESIDUE EDO C 219
23CC5SOFTWAREHIS C:184 , ARG C:187 , ARG C:188BINDING SITE FOR RESIDUE EDO C 220
24CC6SOFTWARECYS C:133 , ASP C:134 , PHE C:136 , ASN C:137BINDING SITE FOR RESIDUE EDO C 221
25CC7SOFTWAREASP B:14 , ARG C:179 , GLU C:180 , HIS C:183BINDING SITE FOR RESIDUE EDO C 222
26CC8SOFTWARETYR A:48 , TRP A:71 , TRP A:72 , ARG A:75 , PEG A:220 , PHE B:192BINDING SITE FOR RESIDUE PEG A 219
27CC9SOFTWAREASP A:21 , ARG A:75 , PEG A:219BINDING SITE FOR RESIDUE PEG A 220
28DC1SOFTWARELEU A:178 , GLU A:180 , HIS A:183 , ARG C:41BINDING SITE FOR RESIDUE PEG A 221
29DC2SOFTWAREARG B:75 , ALA B:76 , ILE B:77 , SER B:78BINDING SITE FOR RESIDUE PEG B 214
30DC3SOFTWAREPRO A:197 , HOH A:236 , ILE B:4 , VAL B:5 , GLN B:42 , PRO B:197 , VAL B:198 , GLY B:199BINDING SITE FOR RESIDUE PEG B 215
31DC4SOFTWAREEDO A:218 , TYR B:48 , TRP B:72 , ARG B:75BINDING SITE FOR RESIDUE PEG B 216
32DC5SOFTWAREARG A:187 , ARG A:188 , ARG A:189 , ASP A:190 , GLY B:118 , HOH B:254 , HOH B:255BINDING SITE FOR RESIDUE PEG B 217
33DC6SOFTWARESER A:209 , ASP B:115 , PRO B:116 , LEU B:117 , PHE B:136 , ARG B:144 , HOH B:257BINDING SITE FOR RESIDUE PEG B 218
34DC7SOFTWAREALA C:76 , ILE C:77 , ARG C:108BINDING SITE FOR RESIDUE PEG C 223

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C3P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C3P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C3P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C3P)

(-) Exons   (0, 0)

(no "Exon" information available for 3C3P)

(-) 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:198
 aligned with Q74FR2_GEOSL | Q74FR2 from UniProtKB/TrEMBL  Length:209

    Alignment length:210
                             1                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
         Q74FR2_GEOSL     - -MIPIVDSRIGAYLDGLLPEADPVVAAMEQIARERNIPIVDRQTGRLLYLLARIKQPQLVVVPGDGLGCASWWFARAISISSRVVMIDPDRDNVEHARRMLHDNGLIDRVELQVGDPLGIAAGQRDIDILFMDCDVFNGADVLERMNRCLAKNALLIAVNALRRGSVAESHEDPETAALREFNHHLSRRRDFFTTIVPVGNGVLLGYRLS 209
               SCOP domains d3c3pa_ A: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 3c3pA00 A:0-209 Vaccinia Virus protein VP39                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhh....eeeeeee....hhhhhhhhhh..eeeeeeeeee......------------..hhhhhhhh....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c3p A   0 GmIPIVDSRIGAYLDGLLPEADPVVAAmEQIARERNIPIVDRQTGRLLYLLARIKQPQLVVVPGDGLGCASWWFARAISISSRVVmIDPDRDNVEHARRmLHDNGLIDRVELQVGDPLGIAAGQRDIDILFmDCDVFNGADVLERmNRCLAKNALLIAVNALRRG------------ALREFNHHLSRRRDFFTTIVPVGNGVLLGYRLS 209
                             |       9        19       |29        39        49        59        69        79     |  89        99       109       119       129 |     139     | 149       159    |    -       179       189       199       209
                             |                        27-MSE                                                    85-MSE        99-MSE                         131-MSE       145-MSE            164          177                                
                             1-MSE                                                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:190
 aligned with Q74FR2_GEOSL | Q74FR2 from UniProtKB/TrEMBL  Length:209

    Alignment length:206
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      
         Q74FR2_GEOSL     3 PIVDSRIGAYLDGLLPEADPVVAAMEQIARERNIPIVDRQTGRLLYLLARIKQPQLVVVPGDGLGCASWWFARAISISSRVVMIDPDRDNVEHARRMLHDNGLIDRVELQVGDPLGIAAGQRDIDILFMDCDVFNGADVLERMNRCLAKNALLIAVNALRRGSVAESHEDPETAALREFNHHLSRRRDFFTTIVPVGNGVLLGYRL 208
               SCOP domains d3c3pb_ B: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains 3c3pB00 B:3-208 Vaccinia Virus protein VP39                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhh....eeeeeee....hhhhhhhhhh..eeeeeeeeee....----------------hhhhhhhh....eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3p B   3 PIVDSRIGAYLDGLLPEADPVVAAmEQIARERNIPIVDRQTGRLLYLLARIKQPQLVVVPGDGLGCASWWFARAISISSRVVmIDPDRDNVEHARRmLHDNGLIDRVELQVGDPLGIAAGQRDIDILFmDCDVFNGADVLERmNRCLAKNALLIAVNALR----------------REFNHHLSRRRDFFTTIVPVGNGVLLGYRL 208
                                    12        22    |   32        42        52        62        72        82  |     92      |102       112       122       132       142  |    152       162         -      |182       192       202      
                                                   27-MSE                                                    85-MSE        99-MSE                         131-MSE       145-MSE          162              179                             

Chain C from PDB  Type:PROTEIN  Length:195
 aligned with Q74FR2_GEOSL | Q74FR2 from UniProtKB/TrEMBL  Length:209

    Alignment length:208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        
         Q74FR2_GEOSL     2 IPIVDSRIGAYLDGLLPEADPVVAAMEQIARERNIPIVDRQTGRLLYLLARIKQPQLVVVPGDGLGCASWWFARAISISSRVVMIDPDRDNVEHARRMLHDNGLIDRVELQVGDPLGIAAGQRDIDILFMDCDVFNGADVLERMNRCLAKNALLIAVNALRRGSVAESHEDPETAALREFNHHLSRRRDFFTTIVPVGNGVLLGYRLS 209
               SCOP domains d3c3pc_ C: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 3c3pC00 C:2-209 Vaccinia Virus protein VP39                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhh....eeeeeee....hhhhhhhhhh..eeeeeeeeee......-------------.hhhhhhhhh...eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c3p C   2 IPIVDSRIGAYLDGLLPEADPVVAAmEQIARERNIPIVDRQTGRLLYLLARIKQPQLVVVPGDGLGCASWWFARAISISSRVVmIDPDRDNVEHARRmLHDNGLIDRVELQVGDPLGIAAGQRDIDILFmDCDVFNGADVLERmNRCLAKNALLIAVNALRRG-------------LREFNHHLSRRRDFFTTIVPVGNGVLLGYRLS 209
                                    11        21     |  31        41        51        61        71        81   |    91       101       111       121       131       141   |   151       161  |      -      |181       191       201        
                                                    27-MSE                                                    85-MSE        99-MSE                         131-MSE       145-MSE            164           178                               

   Legend:   → Mismatch (orange background)
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    → 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  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C3P)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q74FR2_GEOSL | Q74FR2)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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