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(-) Description

Title :  CRYSTAL STRUCTURE OF EPOXYQUEUOSINE REDUCTASE WITH A TRNA-TYR EPOXYQUEUOSINE-MODIFIED TRNA STEM LOOP
 
Authors :  D. P. Dowling, Z. D. Miles, C. Kohrer, V. Bandarian, C. L. Drennan
Date :  03 Aug 15  (Deposition) - 28 Sep 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,F
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  B12, Trna Modification, Heat-Domain, Queuosine, Oxidoreductase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. P. Dowling, Z. D. Miles, C. Kohrer, S. J. Maiocco, S. J. Elliott, V. Bandarian, C. L. Drennan
Molecular Basis Of Cobalamin-Dependent Rna Modification.
Nucleic Acids Res. V. 44 9965 2016
PubMed-ID: 27638883  |  Reference-DOI: 10.1093/NAR/GKW806

(-) Compounds

Molecule 1 - EPOXYQUEUOSINE REDUCTASE
    ChainsA, B
    EC Number1.17.99.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPASK-IBA43PLUS
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneQUEG, YGAP, YHBA, BSU08910
    Organism ScientificBACILLUS SUBTILIS (STRAIN 168)
    Organism Taxid224308
    Strain168
    SynonymQUEUOSINE BIOSYNTHESIS PROTEIN QUEG
 
Molecule 2 - RNA (5'-D(*GP*CP*AP*GP*AP*CP*UP*(56B) P*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
    ChainsF
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsSYNTHESIZED BY IDT AND ENZYMATICALLY MODIFIED
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABF
Biological Unit 1 (1x)A F
Biological Unit 2 (1x) B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
156B1Mod. Nucleotide2-AMINO-5-({[(1S,4S,5R)-4,5-DIHYDROXYCYCLOPENT-2-EN-1-YL]AMINO}METHYL)-7-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE
2B122Ligand/IonCOBALAMIN
3GOL1Ligand/IonGLYCEROL
4PO42Ligand/IonPHOSPHATE ION
5SF44Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (5, 6)
No.NameCountTypeFull Name
156B1Mod. Nucleotide2-AMINO-5-({[(1S,4S,5R)-4,5-DIHYDROXYCYCLOPENT-2-EN-1-YL]AMINO}METHYL)-7-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE
2B121Ligand/IonCOBALAMIN
3GOL1Ligand/IonGLYCEROL
4PO41Ligand/IonPHOSPHATE ION
5SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
156B-1Mod. Nucleotide2-AMINO-5-({[(1S,4S,5R)-4,5-DIHYDROXYCYCLOPENT-2-EN-1-YL]AMINO}METHYL)-7-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-3,7-DIHYDRO-4H-PYRROLO[2,3-D]PYRIMIDIN-4-ONE
2B121Ligand/IonCOBALAMIN
3GOL-1Ligand/IonGLYCEROL
4PO41Ligand/IonPHOSPHATE ION
5SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:153 , LYS A:154 , ASN A:155 , CYS A:188 , CYS A:191 , CYS A:194 , CYS A:247 , LEU A:249binding site for residue SF4 A 501
2AC2SOFTWARECYS A:198 , LEU A:209 , CYS A:214 , ILE A:215 , CYS A:240 , THR A:242 , CYS A:243binding site for residue SF4 A 502
3AC3SOFTWARELEU A:33 , ARG A:36 , SER A:47 , GLU A:50 , ARG A:57 , CYS A:97 , ASP A:134 , LEU A:138 , SER A:139 , ASP A:140 , ARG A:141 , ALA A:142 , SER A:152 , ASN A:155 , MET A:157 , ILE A:158 , SER A:165 , VAL A:167 , LEU A:169 , PRO A:206 , GLY A:207 , LEU A:209 , SER A:216 , GLY A:239 , CYS A:240 , ASP A:241 , GLN A:244 , HOH A:607 , HOH A:608 , 56B F:34binding site for residue B12 A 503
4AC4SOFTWARELYS A:112 , HIS A:258 , GLU A:260binding site for residue PO4 A 504
5AC5SOFTWAREASN A:280 , GLY A:296 , LYS A:297 , C F:32 , A F:36 , HOH F:106binding site for residue GOL A 505
6AC6SOFTWAREALA B:153 , LYS B:154 , ASN B:155 , CYS B:188 , CYS B:191 , CYS B:194 , CYS B:247 , PRO B:248 , LEU B:249binding site for residue SF4 B 501
7AC7SOFTWARECYS B:198 , LEU B:209 , CYS B:214 , ILE B:215 , CYS B:240 , THR B:242 , CYS B:243binding site for residue SF4 B 502
8AC8SOFTWAREGLU A:373 , SER B:32 , LEU B:33 , ARG B:36 , LEU B:37 , SER B:47 , GLU B:50 , ARG B:57 , CYS B:97 , TYR B:105 , ASP B:134 , LEU B:138 , SER B:139 , ASP B:140 , ARG B:141 , ALA B:142 , SER B:152 , ASN B:155 , CYS B:156 , MET B:157 , ILE B:158 , SER B:165 , VAL B:167 , LEU B:169 , PRO B:206 , GLY B:207 , LEU B:209 , SER B:216 , PHE B:217 , GLY B:239 , CYS B:240 , ASP B:241 , CYS B:243 , GLN B:244 , HOH B:614 , HOH B:619binding site for residue B12 B 503
9AC9SOFTWAREILE B:17 , LYS B:112 , LEU B:257 , HIS B:258 , GLU B:260binding site for residue PO4 B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D0B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:125 -Asp A:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D0B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D0B)

(-) Exons   (0, 0)

(no "Exon" information available for 5D0B)

(-) 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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh.........hhhhhhhhhhhh....eeeeeeee..................ee.hhhh..hhhhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhh...ee.....ee.......eeeeeeee.................hhhhhhh...........hhhhhhhhhh......hhhhh.....eee..hhhhhhhhhhh......hhhhh.hhhhhh.hhhhhhh.hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d0b A   2 NVYQLKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEEPDIEKRVTPKLLLPKAKSIVAIALAYPSRMKDAPRSTRTERRGIFCRASWGKDYHDVLREKLDLLEDFLKSKHEDIRTKSMVDTGELSDRAVAERAGIGFSAKNCMITTPEYGSYVYLAEMITNIPFEPDVPIEDMCGSCTKCLDACPTGALVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTCQTVCPLNKGKDFHLHPEMEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQRNAILALAHFKDASALPELTELMHKDPRPVIRGTAAWAIGKIGDPAYAEELEKALEKEKDEEAKLEIEKGIELLKA 377
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371      

Chain B from PDB  Type:PROTEIN  Length:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh.........hhhhhhhhhhhh....eeeeeeee..................ee.hhhh..hhhhhhhhhhhhhhhhhhhh....eeee......hhhhhhhhh...ee.....ee.......eeeeeeee.................hhhhhhh...........hhhhhhhhhh......hhhhh.....eee..hhhhhhhhhhh......hhhhh.hhhhhh.hhhhhhh.hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d0b B   2 NVYQLKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEEPDIEKRVTPKLLLPKAKSIVAIALAYPSRMKDAPRSTRTERRGIFCRASWGKDYHDVLREKLDLLEDFLKSKHDIRTKSMVDTGELSDRAVAERAGIGFSAKNCMITTPEYGSYVYLAEMITNIPFEPDVPIEDMCGSCTKCLDACPTGALVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTCQTVCPLNKGKDFHLHPEMEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQRNAILALAHFKDASALPELTELMHKDPRPVIRGTAAWAIGKIGDPAYAEELEKALEKEKDEEAKLEIEKGIELLKA 377
                                    11        21        31        41        51        61        71        81        91       101       111       121  ||   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372     
                                                                                                                                                    124|                                                                                                                                                                                                                                                           
                                                                                                                                                     126                                                                                                                                                                                                                                                           

Chain F from PDB  Type:RNA  Length:17
                                                 
                 5d0b F  27 GCAGACUxUAAAUCUGC  43
                                   |36       
                                  34-56B     

   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  (0, 0)

(no "SCOP Domain" information available for 5D0B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D0B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D0B)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        QUEG_BACSU | P970305d08 5d0a 5t8y

(-) Related Entries Specified in the PDB File

5d08 5D08 IS THE SAME PROTEIN WITH SELENOMETHIONINE LABELING IN THE ABSENCE OF RNA.
5d0a 5D0A IS THE SAME PROTEIN WITH A CLEAVED RNA STEM LOOP BOUND.