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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRNA (CYTIDINE(34)-2'-O)-METHYLTRANSFERASE BOUND TO S-ADENOSYL HOMOCYSTEINE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  29 Apr 13  (Deposition) - 08 May 13  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Structural Genomics, Niaid, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, National Institute For Allergy And Infectious Disease, Trna Methyltransferase, Trefoil Protein Knot, 3(1) Protein Knot, S-Adenosyl-Methionine-Dependent, Sam, S- Adenosylhomocysteine, Sah, Half-Site Occupancy, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, J. W. Fairman, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of A Trmh Family Trna Methyltransferase Bound To S-Adenosyl Homocysteine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRNA (CYTIDINE(34)-2'-O)-METHYLTRANSFERASE
    Chains: A, B, C, D, E, F, G, H
    EC Number: 2.1.1.207
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BURPS1710B_0668, TRML
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 320372
    Strain: 1710B
    Synonym: TRNA (CYTIDINE/URIDINE-2'-O-)-METHYLTRANSFERASE TRML

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:80 , THR A:81 , THR A:82 , PHE A:101 , GLY A:102 , ALA A:103 , GLU A:104 , THR A:105 , GLY A:107 , LEU A:108 , VAL A:122 , ARG A:123 , LEU A:124 , MET A:126 , SER A:132 , LEU A:133 , THR A:138 , HOH A:341 , HOH A:342 , ASN E:130BINDING SITE FOR RESIDUE SAH A 201
02AC2SOFTWARELEU A:133 , ASN A:134 , ASN A:137 , LEU B:21 , ASN B:24 , HOH B:315BINDING SITE FOR RESIDUE CL A 202
03AC3SOFTWAREGLU B:10 , ILE B:11 , GLU B:104BINDING SITE FOR RESIDUE CL B 201
04AC4SOFTWAREPHE C:80 , THR C:81 , PHE C:101 , GLY C:102 , ALA C:103 , GLU C:104 , THR C:105 , GLY C:107 , LEU C:108 , VAL C:122 , ARG C:123 , LEU C:124 , MET C:126 , SER C:132 , LEU C:133 , THR C:138 , HOH C:341 , HOH C:360BINDING SITE FOR RESIDUE SAH C 201
05AC5SOFTWARELEU C:133 , ASN C:134 , ASN C:137 , LEU D:21 , ASN D:24 , HOH D:205BINDING SITE FOR RESIDUE CL C 202
06AC6SOFTWAREASN A:130 , PHE E:80 , THR E:81 , THR E:82 , PHE E:101 , GLY E:102 , ALA E:103 , GLU E:104 , THR E:105 , ARG E:106 , GLY E:107 , LEU E:108 , VAL E:122 , ARG E:123 , LEU E:124 , MET E:126 , SER E:132 , LEU E:133 , THR E:138 , HOH E:321 , HOH E:336BINDING SITE FOR RESIDUE SAH E 201
07AC7SOFTWARELEU E:133 , ASN E:134 , ASN E:137 , LEU F:21 , ASN F:24 , HOH F:309BINDING SITE FOR RESIDUE CL E 202
08AC8SOFTWAREGLU F:10 , ILE F:11 , GLU F:104 , HOH F:303BINDING SITE FOR RESIDUE CL F 201
09AC9SOFTWAREPHE G:80 , THR G:81 , PHE G:101 , GLY G:102 , ALA G:103 , GLU G:104 , GLY G:107 , VAL G:122 , ARG G:123 , LEU G:124 , MET G:126 , SER G:132 , LEU G:133 , THR G:138 , HOH G:332BINDING SITE FOR RESIDUE SAH G 201
10BC1SOFTWARELEU G:133 , ASN G:134 , ASN G:137 , LEU H:21 , ASN H:24 , HOH H:214BINDING SITE FOR RESIDUE CL G 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Glu A:33 -Pro A:34
2Glu B:33 -Pro B:34
3Glu C:33 -Pro C:34
4Glu D:33 -Pro D:34
5Glu E:33 -Pro E:34
6Glu F:33 -Pro F:34
7Glu G:33 -Pro G:34
8Glu H:33 -Pro H:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KGN)

(-) 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:139
                                                                                                                                                                           
               SCOP domains d4kgna_ A: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhhh.eeeee.......eeee.hhhhhhhhhh.hhh.eeee.....ee..........eeee.......hhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgn A   1 MFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPQMRVHRDWDAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAWRQAGFEGGA 156
                                    10        20        30       |57        67        77        87        97       107       117       127       137       147         
                                                                38|                                                                                                    
                                                                 56                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains d4kgnb_ B: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..hhhhhh..eee.hhhhhhhhhh.hhh.eeee.....ee.hhh......eeee.......hhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kgn B   1 MFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRDWDAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAWRQAGFEGGA 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      


Chain C from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains d4kgnc_ C: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..hhhhhh..eee.hhhhhhhhhh.hhh.eeee.....ee..........eeee.......hhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgn C   0 SMFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRDWDAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAWRQAGFEGGA 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       


Chain D from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains d4kgnd_ D: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhh.eeeee.........hhhhhhh.eee.hhhhhhhhhh.hhh.eeee.....ee.hhh......eeee.......hhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kgn D  -1 GSMFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLGLDYHEYAQMRVHRDWDAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAWRQAGFEGGA 156
                                     8        18        28        38||      56        66        76        86        96       106       116       126       136       146       156
                                                                   39|                                                                                                            
                                                                    48                                                                                                            


Chain E from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains d4kgne_ E: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..hhhhhh..eee.hhhhhhhhhh.hhh.eeee.....ee..........eeee.......hhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kgn E   1 MFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRDWDAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAWRQAGFEGGA 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      


Chain F from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains d4kgnf_ F: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..hhhhhh..eee.hhhhhhhhhh.hhh.eeee.....ee.hhh......eeee.......hhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgn F  -1 GSMFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRDWDAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAWRQAGFEGGA 156
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148        


Chain G from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains d4kgng_ G: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhhh.eeeee..........hhhhhh.eee.hhhhhhhhhh.hhh.eeee.....ee..........eeee.......hhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgn G   1 MFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLGLDYHEYAQMRVHRDWDAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAWRQAGFEGGA 156
                                    10        20        30        48        58        68        78        88        98       108       118       128       138       148        
                                                                 39|                                                                                                            
                                                                  48                                                                                                            


Chain H from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains d4kgnh_ H: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..hhhhhh..eee.hhhhhhhhhh.hhh.eeee.....ee.hhh......eeee.......hhhhhhhhhhh.eee..........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kgn H   1 MFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRDWDAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAWRQAGFEGGA 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   Legend:   → Mismatch (orange background)
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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  (2, 8)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3e5y APO STRUCTURE RELATED ID: BUPSA.00072.A RELATED DB: TARGETTRACK