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(-) Description

Title :  CRYSTAL STRUCTURE OF A SYMMETRIC DIMER OF A TRNA (GUANINE-(N(1)-)-METHYLTRANSFERASE FROM BURKHOLDERIA PHYMATUM BOUND TO S-ADENOSYL HOMOCYSTEIN IN BOTH HALF-SITES
 
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 :  2.15
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, Trna Methylation, M1G37 Methylation, Transferase, Sah, Sam, Food Parasite (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, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
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 , GLY A:144 , GLY A:145 , PRO A:148 , HOH A:414 , HOH A:445 , HOH A:467 , ASP B:173 , SER B:174 , ASP B:181 , HOH B:468BINDING SITE FOR RESIDUE SAH A 301
2AC2SOFTWAREHIS A:100 , HIS A:159 , PHE B:140 , VAL B:141BINDING SITE FOR RESIDUE CL A 302
3AC3SOFTWAREPHE A:140 , VAL A:141 , HIS B:100 , HIS B:159BINDING SITE FOR RESIDUE CL A 303
4AC4SOFTWAREASP A:173 , SER A:174 , ASP A:181 , MET B:91 , SER B:92 , PRO B:93 , GLY B:117 , TYR B:119 , GLU B:120 , VAL B:135 , SER B:136 , LEU B:137 , GLY B:138 , PHE B:140 , LEU B:142 , GLY B:144 , GLY B:145 , PRO B:148 , HOH B:442 , HOH B:444BINDING SITE FOR RESIDUE SAH B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H3Z)

(-) 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 4H3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4H3Z)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains d4h3za_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhh.......ee.........eehhhhhhhhhhhhhhhhhhh.....eeeee....ee.hhhhhhhhhh..eeeee.....eehhhhhhhhh.eeee........hhhhhhhhhhhhhhh........................ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h3z A   0 SMQFDIVTLFPDMFRALTDWGITSRAAKQERYGLRTWNPRDFTTDNYRTIDDRPYGGGPGMVMLARPLEDAINAAKAAQAEQGIGGARVVMMSPQGATLNHDKVMRFAAEPGLILLCGRYEAIDQRLIDRVVDEEVSLGDFVLSGGELPAMALIDAVVRHLPGVLNQDSFVDGLLDCPHYTRPEEYDGVRVPDVLLGGHHAEIEQWRRREALRNTWLKRPDLIVQARKNKLLSRADEAWLASLAKDASK 254
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159     ||175       185       195       205       215       225       235       245         
                                                                                                                                                                                               165|                                                                                  
                                                                                                                                                                                                172                                                                                  


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4h3zb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeehhhhh........ee.........eehhhhhhhhhhhhhhhhhhh.....eeeee....ee.hhhhhhhhhh..eeeee.....eehhhhhhhhh.eeee........hhhhhhhhhhhhhh......hhhhhhh..................ee..ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h3z B  -1 GSMQFDIVTLFPDMFRALTDWGITSRAAKQERYGLRTWNPRDFTTDNYRTIDDRPYGGGPGMVMLARPLEDAINAAKAAQAEQGIGGARVVMMSPQGATLNHDKVMRFAAEPGLILLCGRYEAIDQRLIDRVVDEEVSLGDFVLSGGELPAMALIDAVVRHLPGVLNDAQSAVQDSFVDGLLDCPHYTRPEEYDGVRVPDVLLGGHHAEIEQWRRREALRNTWLKRPDLIVQARKNKLLSRADEAWLASLAKDASK 254
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H3Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H3Z)

(-) 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: 4h3y

(-) Related Entries Specified in the PDB File

4h3y ASYMMETRIC DIMER WITH APO/SAH HALF-SITES RELATED ID: BUPHA.00054.A RELATED DB: TARGETTRACK