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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ASYMMETRIC DIMER OF A TRNA (GUANINE-(N(1)-)-METHYLTRANSFERASE FROM BURKHOLDERIA PHYMATUM BOUND TO S-ADENOSYL HOMOCYSTEIN IN ONE HALF-SITE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  14 Sep 12  (Deposition) - 03 Oct 12  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Trmd, M1G-Methyltransferase, G37 Methyltransferase, S-Adenosyl-Methionine, Sam, S-Adenosyl- Homocysteine, Sah, Trna Modification, Transferase, Proteobacteria, Nitrogen Fixation, Food Pathogen, Domain Swapped Homodimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053851

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.228
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PAVA0421
    Gene: BPHY_0771, TRMD
    Organism Scientific: BURKHOLDERIA PHYMATUM
    Organism Taxid: 391038
    Strain: DSM 17167 STM815
    Synonym: M1G-METHYLTRANSFERASE, TRNA [GM37] METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:91 , SER A:92 , PRO A:93 , GLY A:117 , TYR A:119 , GLU A:120 , VAL A:135 , SER A:136 , LEU A:137 , GLY A:138 , PHE A:140 , LEU A:142 , SER A:143 , GLY A:144 , GLY A:145 , PRO A:148 , HOH A:416 , ASP B:173 , SER B:174BINDING SITE FOR RESIDUE SAH A 301
2AC2SOFTWAREHIS A:100 , HIS A:159 , VAL B:141BINDING SITE FOR RESIDUE CL A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H3Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:187 -Pro A:188
2Arg B:187 -Pro B:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H3Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H3Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4H3Y)

(-) 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:255
                                                                                                                                                                                                                                                                                               
               SCOP domains d4h3ya_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhh.......ee.........eehhhhhhhhhhhhhhhhhh......eeeee....ee.hhhhhhhhhhh.eeeee.....eehhhhhhhhh.eeee........hhhhhhhhhhhhhh.......hhhhhhhhh...............ee..ee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h3y A   0 SMQFDIVTLFPDMFRALTDWGITSRAAKQERYGLRTWNPRDFTTDNYRTIDDRPYGGGPGMVMLARPLEDAINAAKAAQAEQGIGGARVVMMSPQGATLNHDKVMRFAAEPGLILLCGRYEAIDQRLIDRVVDEEVSLGDFVLSGGELPAMALIDAVVRHLPGVLNDAQSAVQDSFVDGLLDCPHYTRPEEYDGVRVPDVLLGGHHAEIEQWRRREALRNTWLKRPDLIVQARKNKLLSRADEAWLASLAKDASK 254
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249     


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains d4h3yb_ B: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhh.hhhhhhhhh..eeeeeehhhhhh.......ee.........eehhhhhhhhhhhhhhhhhh.......eeee....ee.hhhhhhhhhh..eeeeee....eehhhhhhhhh.eeee........hhhhhhhhhhhhhh......hhhhhhh.................ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h3y B   0 SMQFDIVTLFPDMFRALTDWGITSRAAKQERYGLRTWNPRDFTTDNYRTIDDRPYGGGPGMVMLARPLEDAINAAKAAQAEQGIGGARVVMMSPQGATLNHDKVMRFAAEPGLILLCGRYEAIDQRLIDRVVDEEVSLGDFVLSGGELPAMALIDAVVRHLPGVLNDAQSAVDSFVDGLLDCPHYTRPEEYDGVRVPDVLLGGHHAEIEQWRRREALRNTWLKRPDLIVQARKNKLLSRADEAWLASLAKDASK 254
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 ||    180       190       200       210       220       230       240       250    
                                                                                                                                                                                                     171|                                                                                 
                                                                                                                                                                                                      173
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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 4H3Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H3Y)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:187 - Pro A:188   [ RasMol ]  
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  2.1.1.228
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TRMD_PARP8 | B2JF31: 4h3z

(-) Related Entries Specified in the PDB File

4h3z SAME PROTEIN AS SYMMETRIC DIMER WITH SAH IN BOTH HALF-SITES RELATED ID: BUPHA.00054.A RELATED DB: TARGETTRACK