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(-) Description

Title :  E. COLI DIHYDROURIDINE SYNTHASE C (DUSC) IN COMPLEX WITH TRNAPHE
 
Authors :  R. T. Byrne, H. T. Jenkins, D. T. Peters, F. Whelan, J. Stowell, N. Aziz, P. Kasatsky, M. V. Rodnina, E. V. Koonin, A. L. Konevega, A. A. Antson
Date :  20 Feb 15  (Deposition) - 22 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Trna Modification, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Byrne, H. T. Jenkins, D. T. Peters, F. Whelan, J. Stowell, N. Aziz, P. Kasatsky, M. V. Rodnina, E. V. Koonin, A. L. Konevega, A. A. Antson
Major Reorientation Of Trna Substrates Defines Specificity Of Dihydrouridine Synthases.
Proc. Natl. Acad. Sci. Usa V. 112 6033 2015
PubMed-ID: 25902496  |  Reference-DOI: 10.1073/PNAS.1500161112

(-) Compounds

Molecule 1 - TRNA-DIHYDROURIDINE SYNTHASE C
    Chains: A, B, C
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DUSC, YOHI, B2140, JW2128
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
 
Molecule 2 - TRNAPHE
    Chains: D, E, F
    Engineered: YES
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 31)

Asymmetric Unit (3, 31)
No.NameCountTypeFull Name
1FMN3Ligand/IonFLAVIN MONONUCLEOTIDE
2MG25Ligand/IonMAGNESIUM ION
3MN3Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2MG-1Ligand/IonMAGNESIUM ION
3MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2MG-1Ligand/IonMAGNESIUM ION
3MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2MG-1Ligand/IonMAGNESIUM ION
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:6 , PRO A:7 , MET A:8 , GLU A:9 , PHE A:33 , GLN A:68 , ASN A:95 , LYS A:139 , HIS A:168 , TYR A:176 , ASN A:200 , GLY A:201 , GLU A:202 , GLY A:224 , ARG A:225 , HOH A:511 , HOH A:513 , HOH A:551 , U D:16binding site for residue FMN A 401
02AC2SOFTWAREHOH B:513 , HOH B:514 , HOH E:212 , HOH E:213binding site for residue MG B 401
03AC3SOFTWAREALA B:6 , PRO B:7 , MET B:8 , GLU B:9 , PHE B:33 , GLN B:68 , ASN B:95 , LYS B:139 , HIS B:168 , TYR B:176 , ASN B:200 , GLY B:201 , GLU B:202 , GLY B:224 , ARG B:225 , HOH B:526 , HOH B:543 , HOH B:578 , U E:16binding site for residue FMN B 402
04AC4SOFTWAREALA C:6 , PRO C:7 , MET C:8 , GLU C:9 , PHE C:33 , GLN C:68 , ASN C:95 , LYS C:139 , HIS C:168 , TYR C:176 , ASN C:200 , GLY C:201 , GLU C:202 , GLY C:224 , ARG C:225 , HOH C:513 , HOH C:566 , HOH C:567 , U F:16binding site for residue FMN C 401
05AC5SOFTWAREG D:15 , HOH D:249 , HOH D:250 , HOH D:251 , HOH D:253 , HOH D:254binding site for residue MN D 101
06AC6SOFTWAREHOH D:215 , HOH D:216 , HOH D:217 , HOH D:218 , HOH D:219 , HOH D:220binding site for residue MG D 102
07AC7SOFTWAREU D:51 , HOH D:221 , HOH D:222 , HOH D:223 , HOH D:224 , HOH D:225binding site for residue MG D 103
08AC8SOFTWAREHOH D:226 , HOH D:227 , HOH D:228 , HOH D:229 , HOH D:230 , HOH D:231binding site for residue MG D 104
09AC9SOFTWAREHOH D:232 , HOH D:233 , HOH D:234 , HOH D:235 , HOH D:236 , HOH D:237binding site for residue MG D 105
10AD1SOFTWAREG D:18 , HOH D:201 , HOH D:212 , HOH D:214 , HOH D:238 , HOH D:239binding site for residue MG D 106
11AD2SOFTWAREHOH A:501 , C D:17 , G D:19 , HOH D:240 , HOH D:241 , HOH D:242binding site for residue MG D 107
12AD3SOFTWAREHOH D:211 , G E:34 , HOH E:201 , HOH E:202 , HOH E:204binding site for residue MG D 108
13AD4SOFTWAREU D:45 , G D:46 , HOH D:243binding site for residue MG D 109
14AD5SOFTWAREG E:15 , HOH E:246 , HOH E:247 , HOH E:256 , HOH E:257binding site for residue MN E 101
15AD6SOFTWAREHOH E:206 , HOH E:207 , HOH E:208 , HOH E:209 , HOH E:210 , HOH E:211binding site for residue MG E 102
16AD7SOFTWAREG E:18 , HOH E:214 , HOH E:215 , HOH E:216 , HOH E:217binding site for residue MG E 103
17AD8SOFTWAREG E:22 , G E:44 , U E:45 , G E:46 , HOH E:218 , HOH E:219binding site for residue MG E 104
18AD9SOFTWAREHOH E:220 , HOH E:221 , HOH E:222 , HOH E:223 , HOH E:224 , HOH E:225binding site for residue MG E 105
19AE1SOFTWAREHOH B:515 , C E:17 , G E:19 , HOH E:226 , HOH E:227 , HOH E:228binding site for residue MG E 106
20AE2SOFTWAREU E:51 , HOH E:229 , HOH E:230 , HOH E:231 , HOH E:232 , HOH E:233binding site for residue MG E 107
21AE3SOFTWAREU E:8 , U E:12 , HOH E:234 , HOH E:235 , HOH E:236 , HOH E:237 , HOH E:238binding site for residue MG E 108
22AE4SOFTWAREHOH E:239 , HOH E:240 , HOH E:241 , HOH E:242 , HOH E:243 , HOH E:244binding site for residue MG E 109
23AE5SOFTWAREG F:15 , HOH F:253 , HOH F:254 , HOH F:255 , HOH F:256 , HOH F:292binding site for residue MN F 101
24AE6SOFTWAREHOH F:208 , HOH F:209 , HOH F:210 , HOH F:211 , HOH F:212 , HOH F:213binding site for residue MG F 102
25AE7SOFTWAREHOH F:214 , HOH F:215 , HOH F:216 , HOH F:217 , HOH F:218 , HOH F:219binding site for residue MG F 103
26AE8SOFTWAREU F:51 , HOH F:220 , HOH F:221 , HOH F:222 , HOH F:223 , HOH F:224binding site for residue MG F 104
27AE9SOFTWAREHOH D:213 , G F:18 , HOH F:201 , HOH F:207 , HOH F:225 , HOH F:226binding site for residue MG F 105
28AF1SOFTWAREU F:45 , G F:46 , HOH F:227 , HOH F:228 , HOH F:229 , HOH F:230binding site for residue MG F 106
29AF2SOFTWAREU F:12 , HOH F:231 , HOH F:232 , HOH F:233 , HOH F:234 , HOH F:235binding site for residue MG F 107
30AF3SOFTWAREHOH F:236 , HOH F:237 , HOH F:238 , HOH F:239 , HOH F:240binding site for residue MG F 108
31AF4SOFTWAREHOH C:511 , C F:17 , G F:19 , HOH F:241 , HOH F:242 , HOH F:243binding site for residue MG F 109

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YCO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YCO)

(-) 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:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhh....eeeeeeee......hhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeee.hhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yco A   0 SMRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCGAPSGSGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQHVRVLNNSPDIARAIQAIDIEK 314
                                     9        19        29        39        49        59        69        79        89        99||     113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313 
                                                                                                                              100|                                                                                                                                                                                                                 
                                                                                                                               105                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhh....eeeeeeee......hhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeee.hhhhhh.hhhhhhhhh....hhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yco B   0 SMRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCGAPSGSGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQHVRVLNNSPDIARAIQAIDI 312
                                     9        19        29        39        49        59        69        79        89        99||     113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
                                                                                                                              100|                                                                                                                                                                                                               
                                                                                                                               105                                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhh....eeeeeeee......hhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeee.hhhhhh.hhhhhhhhh....hhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yco C   0 SMRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCGAPSGSGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQHVRVLNNSPDIARAIQAIDIEK 314
                                     9        19        29        39        49        59        69        79        89        99||     113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313 
                                                                                                                              100|                                                                                                                                                                                                                 
                                                                                                                               105                                                                                                                                                                                                                 


Chain D from PDB  Type:RNA  Length:74
                                                                                                          
                 4yco D   1 GCGCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGCGCAC  74
                                    10        20        30        40        50        60        70    


Chain E from PDB  Type:RNA  Length:67
                                                                                                   
                 4yco E   3 GCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCG  69
                                    12        22        32        42        52        62       


Chain F from PDB  Type:RNA  Length:71
                                                                                                       
                 4yco F   1 GCGCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUUCCGAGUCCGCG  71
                                    10        20        30        40        50        60        70
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  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 4YCO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUSC_ECOLI | P33371: 3w9z 4bf9 4bfa 4ycp

(-) Related Entries Specified in the PDB File

4bf9 4BF9 CONTAINS WILD-TYPE PROTEIN IN THE ABSENCE OF RNA.
4bfa 4BFA CONTAINS WILD-TYPE PROTEIN IN THE ABSENCE OF RNA.