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(-) Description

Title :  STRUCTURE OF EPOXYQUEUOSINE REDUCTASE FROM BACILLUS SUBTILIS WITH THE ASP134 CATALYTIC LOOP SWUNG OUT OF THE ACTIVE SITE.
 
Authors :  D. P. Dowling, Z. D. Miles, C. Kohrer, S. J. Maiocco, S. J. Elliott, V. Ban C. L. Drennan
Date :  08 Sep 16  (Deposition) - 28 Sep 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,X
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,X  (1x)
Keywords :  B12, Cobalamin, Iron Sulfur Cluster, Trna Modifying Enzyme, 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
    Chains: A, B
    EC Number: 1.17.99.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: QUEG, YGAP, YHBA, BSU08910
    Organism Scientific: BACILLUS SUBTILIS (STRAIN 168)
    Organism Taxid: 224308
    Strain: 168
    Synonym: QUEUOSINE BIOSYNTHESIS PROTEIN QUEG
 
Molecule 2 - RNA (5'- R(*GP*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
    Chains: X
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: ANTICODON STEM LOOP OF TYR-TRNA FROM E. COLI
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABX
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  BX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1B122Ligand/IonCOBALAMIN
2PO47Ligand/IonPHOSPHATE ION
3SF44Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1B121Ligand/IonCOBALAMIN
2PO42Ligand/IonPHOSPHATE ION
3SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1B121Ligand/IonCOBALAMIN
2PO45Ligand/IonPHOSPHATE ION
3SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:153 , LYS A:154 , ASN A:155 , CYS A:188 , CYS A:191 , CYS A:194 , CYS A:247 , PRO A:248binding site for residue SF4 A 501
02AC2SOFTWARECYS A:198 , LEU A:209 , CYS A:214 , ILE A:215 , CYS A:240 , THR A:242 , CYS A:243 , B12 A:503binding site for residue SF4 A 502
03AC3SOFTWARESER A:32 , LEU A:33 , ARG A:36 , SER A:47 , GLU A:50 , ARG A:57 , CYS A:97 , TYR A:105 , LEU A:138 , SER A:139 , ASP A:140 , ARG A:141 , ALA A:142 , SER A:152 , ASN A:155 , 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 , CYS A:243 , GLN A:244 , SF4 A:502 , PO4 A:505 , HOH A:601binding site for residue B12 A 503
04AC4SOFTWARELYS A:354binding site for residue PO4 A 504
05AC5SOFTWAREMET A:132 , VAL A:133 , ASP A:134 , ASP A:140 , B12 A:503binding site for residue PO4 A 505
06AC6SOFTWAREALA B:153 , LYS B:154 , ASN B:155 , CYS B:188 , CYS B:191 , CYS B:194 , CYS B:247 , PRO B:248binding site for residue SF4 B 501
07AC7SOFTWARECYS B:198 , LEU B:209 , CYS B:214 , ILE B:215 , CYS B:240 , THR B:242 , CYS B:243 , B12 B:503binding site for residue SF4 B 502
08AC8SOFTWARESER B:32 , LEU B:33 , ARG B:36 , SER B:47 , GLU B:50 , ARG B:57 , CYS B:97 , ALA B:99 , LEU B:138 , SER B:139 , ASP B:140 , ARG B:141 , ALA B:142 , GLU B:145 , SER B:152 , ASN B:155 , 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 , GLY B:239 , CYS B:240 , ASP B:241 , CYS B:243 , GLN B:244 , SF4 B:502 , PO4 B:508 , HOH B:602binding site for residue B12 B 503
09AC9SOFTWARELYS B:354binding site for residue PO4 B 504
10AD1SOFTWAREPO4 B:506binding site for residue PO4 B 505
11AD2SOFTWARETHR B:245 , PO4 B:505 , PO4 B:507binding site for residue PO4 B 506
12AD3SOFTWARETHR B:242 , THR B:245 , PO4 B:506binding site for residue PO4 B 507
13AD4SOFTWAREHIS B:106 , MET B:132 , GLY B:136 , ASP B:140 , B12 B:503binding site for residue PO4 B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T8Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:135 -Gly A:136
2Glu B:125 -Asp B:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5T8Y)

(-) 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:374
                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh.........hhhhhhhhhhhh....eeeeeeee..................ee.hhhh..hhhhhhhhhhhhhhhhhhhh.....eee.......hhhhhhhh....ee.....ee.......eeeeeeee.................hhhhhhh...............hhhhhh......hhhhhh....eee..hhhhhhhhhhh......hhhhh.hhhhhh..hhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t8y A   2 NVYQLKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEEPDIEKRVTPKLLLPKAKSIVAIALAYPSRMKDAPRSTRTERRGIFCRASWGKDYHDVLREKLDLLEDFLKSKHEDIRTKSMVDTGELSDRAVAERAGIGFSAKNCMITTPEYGSYVYLAEMITNIPFEPDVPIEDMCGSCTKCLDACPTGALVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTCQTVCPLNKGKDFHLHPEMEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQRNAILALAHFKDASALPELTELMHKDPRPVIRGTAAWAIGKIGDPAYAEELEKALEKEKDEEAKLEIEKGIELL 375
                                    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:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh.........hhhhhhhhhhhh....eeeeeeee..................ee.hhhh..hhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhh....ee.....ee.......eeeeeeee.................hhhhhhh...............hhhhhh................eee..hhhhhhhhhhh............hhhhhh.hhhhhh..hhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t8y B   2 NVYQLKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEEPDIEKRVTPKLLLPKAKSIVAIALAYPSRMKDAPRSTRTERRGIFCRASWGKDYHDVLREKLDLLEDFLKSKHEDIRTKSMGELSDRAVAERAGIGFSAKNCMITTPEYGSYVYLAEMITNIPFEPDVPIEDMCGSCTKCLDACPTGALVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTCQTVCPLNKGKDFHLHPEMEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQRNAILALAHFKDASALPELTELMHKDPRPVIRGTAAWAIGKIGDPAYAEELEKALEKEKDEEAKLEIEKGIELLK 376
                                    11        21        31        41        51        61        71        81        91       101       111       121       131||     144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374  
                                                                                                                                                            132|                                                                                                                                                                                                                                                
                                                                                                                                                             136                                                                                                                                                                                                                                                


Chain X from PDB  Type:RNA  Length:5
                                     
                 5t8y X  29 AGACU  33
   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  (0, 0)

(no "SCOP Domain" information available for 5T8Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T8Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T8Y)

(-) Gene Ontology  (9, 9)

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        QUEG_BACSU | P97030: 5d08 5d0a 5d0b

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