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(-) Description

Title :  CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE TRNA RIBOSYLTRANSFERASE (TM0574) FROM THERMOTOGA MARITIMA AT 2.00 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  28 Jun 04  (Deposition) - 17 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tm0574, S-Adenosylmethionine Trna Ribosyltransferase, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Mathews, R. Schwarzenbacher, D. Mcmullan, P. Abdubek, E. Ambing, H. Axelrod, T. Biorac, J. M. Canaves, H. J. Chiu, A. M. Deacon, M. Didonato, M. A. Elsliger, A. Godzik, C. Grittini, S. K. Grzechnik, J. Hale, E. Hampton, G. W. Han, J. Haugen, M. Hornsby, L. Jaroszewski, H. E. Klock, E. Koesema, A. Kreusch, P. Kuhn, S. A. Lesley, I. Levin, M. D. Miller, K. Moy, E. Nigoghossian, J. Ouyang, J. Paulsen, K. Quijano, R. Reyes, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, A. White, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of S-Adenosylmethionine:Trna Ribosyltransferase-Isomerase (Quea) From Thermotoga Maritim At 2. 0 A Resolution Reveals A New Fold.
Proteins V. 59 869 2005
PubMed-ID: 15822125  |  Reference-DOI: 10.1002/PROT.20419

(-) Compounds

Molecule 1
    Chains: A, B
    EC Number: 5.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: QUEA, TM0574
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: QUEUOSINE BIOSYNTHESIS PROTEIN QUEA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:174 , ALA A:175 , GLY A:248 , THR A:249 , THR A:250 , THR A:289 , ASN A:290 , HIS A:292 , LEU A:298BINDING SITE FOR RESIDUE UNL A 350
2AC2SOFTWARETHR B:174 , ALA B:175 , GLY B:248 , THR B:249 , THR B:250 , THR B:289 , ASN B:290 , HIS B:292 , LEU B:298BINDING SITE FOR RESIDUE UNL B 350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VKY)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Glu A:21 -Pro A:22
2Arg A:96 -Pro A:97
3Gln A:131 -Pro A:132
4Pro A:277 -Pro A:278
5Glu B:21 -Pro B:22
6Arg B:96 -Pro B:97
7Gln B:131 -Pro B:132
8Pro B:277 -Pro B:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VKY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VKY)

(-) Exons   (0, 0)

(no "Exon" information available for 1VKY)

(-) 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:280
 aligned with QUEA_THEMA | Q9WZ44 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:332
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  
           QUEA_THEMA     4 SEFDYELPPELIAQEPVEPRDASRLMVLHRKTQRIEHRIFREIIEYLEPGDLLVLNVSKVIPARLYARKKTGASIEILLIERLEEGIWKCLVRPGQKVKKGTELVIDEDLSAVCLGRGEDGTRILKFQPQDDRLIFEKGRTPLPPYIKNEVPLERYQTVYAKEEGSVAAPTAGLHFTPELIEKLKKKGVQFAEVVLHVGIGTFRPVKVEEVEKHKMHEEFYQVPKETVRKLRETRERGNRIVAVGTTTVRTLETIARLPEQEEYVGKTDLFIYPPFEFKLVDALVTNFHLPRSTLLMLVAAFAGKDFVMEAYREAVKRRYRFFSFGDAMLIL 335
               SCOP domains d1vkya_ A: Queuosine biosynthesis protein queA                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh......hhhh.eeeeee....eeeeee.hhhhhhh....eeeeeeeee...eeee..---..eeeeeeeeee..eeeeeee.........eeeee..eeeeeeee.....eeeeee..hhhhhhhhh-------------------------------hhhhhhhhhhhhhhhhhh.eeeeeeeee------------------...eeeehhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.......eee................eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vky A   4 SEFDYELPPELIAQEPVEPRDASRLMVLHRKTQRIEHRIFREIIEYLEPGDLLVLNVSKVIPARLYARK---ASIEILLIERLEEGIWKCLVRPGQKVKKGTELVIDEDLSAVCLGRGEDGTRILKFQPQDDRLIFEKG-------------------------------TAGLHFTPELIEKLKKKGVQFAEVVLHV------------------HEEFYQVPKETVRKLRETRERGNRIVAVGTTTVRTLETIARLPEQEEYVGKTDLFIYPPFEFKLVDALVTNFHLPRSTLLMLVAAFAGKDFVMEAYREAVKRRYRFFSFGDAMLIL 335
                                    13        23        33        43        53        63        |-  |     83        93       103       113       123       133        |-         -         -         -|      183       193       | -         -      |223       233       243       253       263       273       283       293       303       313       323       333  
                                                                                               72  76                                                               142                             174                        201                220                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with QUEA_THEMA | Q9WZ44 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:332
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  
           QUEA_THEMA     4 SEFDYELPPELIAQEPVEPRDASRLMVLHRKTQRIEHRIFREIIEYLEPGDLLVLNVSKVIPARLYARKKTGASIEILLIERLEEGIWKCLVRPGQKVKKGTELVIDEDLSAVCLGRGEDGTRILKFQPQDDRLIFEKGRTPLPPYIKNEVPLERYQTVYAKEEGSVAAPTAGLHFTPELIEKLKKKGVQFAEVVLHVGIGTFRPVKVEEVEKHKMHEEFYQVPKETVRKLRETRERGNRIVAVGTTTVRTLETIARLPEQEEYVGKTDLFIYPPFEFKLVDALVTNFHLPRSTLLMLVAAFAGKDFVMEAYREAVKRRYRFFSFGDAMLIL 335
               SCOP domains d1vkyb_ B: Queuosine biosynthesis protein queA                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Queuosine_synth-1vkyB01 B:4-335                                                                                                                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) Queuosine_synth-1vkyB02 B:4-335                                                                                                                                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author .......hhhhh......hhhh.eeeeee....eeeeee.hhhhhhh....eeeeeeeee...eeeee.--..eeeeeeeeeee..eeeeeee.........eeeee..eeeeeeee.....eeeeee..hhhhhhhhh-------------------------------hhhhhhhhhhhhhhhhhh.eeeeeeeee..----------------..eeeeehhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.......eee................eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.........eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vky B   4 SEFDYELPPELIAQEPVEPRDASRLMVLHRKTQRIEHRIFREIIEYLEPGDLLVLNVSKVIPARLYARK--GASIEILLIERLEEGIWKCLVRPGQKVKKGTELVIDEDLSAVCLGRGEDGTRILKFQPQDDRLIFEKG-------------------------------TAGLHFTPELIEKLKKKGVQFAEVVLHVGI----------------HEEFYQVPKETVRKLRETRERGNRIVAVGTTTVRTLETIARLPEQEEYVGKTDLFIYPPFEFKLVDALVTNFHLPRSTLLMLVAAFAGKDFVMEAYREAVKRRYRFFSFGDAMLIL 335
                                    13        23        33        43        53        63        |- |      83        93       103       113       123       133        |-         -         -         -|      183       193       203         -      |223       233       243       253       263       273       283       293       303       313       323       333  
                                                                                               72 75                                                                142                             174                          203              220
   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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VKY)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Queuosine_synth] (3)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (QUEA_THEMA | Q9WZ44)
molecular function
    GO:0051075    S-adenosylmethionine:tRNA ribosyltransferase-isomerase activity    Catalysis of the reaction: S-adenosylmethionine + 7-(aminomethyl)-7-deazaguanosine-tRNA = adenine + methionine + epoxyqueuosine-tRNA. 7-(aminomethyl)-7-deazaguanosine-tRNA is also known as preQ1-tRNA, and epoxyqueuosine-tRNA as oQ-tRNA.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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:0008616    queuosine biosynthetic process    The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents.
    GO:0002099    tRNA wobble guanine modification    The process in which a guanine in t position 34 of a tRNA is post-transcriptionally modified.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1vky
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