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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI WRBA IN COMPLEX WITH BENZOQUINONE
 
Authors :  O. Degtjarik, J. Brynda, O. Ettrichova, J. Carey, I. Kuta Smatanova, R
Date :  13 Mar 15  (Deposition) - 25 May 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.33
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Flavin Mononucleotide, Nad(P)H Dehydrogenase (Quinone), Oxidation- Reduction, Protein Binding, Repressor Proteins, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Degtjarik, J. Brynda, O. Ettrichova, M. Kuty, D. Sinha, I. Kuta Smatanova, J. Carey, R. Ettrich, D. Reha
Quantum Calculations Indicate Effective Electron Transfer Between Fmn And Benzoquinone In A New Crystal Structure Of Escherichia Coli Wrba.
J. Phys. Chem. B V. 120 4867 2016
PubMed-ID: 27183467  |  Reference-DOI: 10.1021/ACS.JPCB.5B11958

(-) Compounds

Molecule 1 - NAD(P)H DEHYDROGENASE (QUINONE)
    Chains: A, B
    EC Number: 1.6.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: WRBA, B1004, JW0989
    Nad(p)h: QUINONE OXIDOREDUCTASE
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2MHO2Mod. Amino AcidS-OXYMETHIONINE
3PLQ2Ligand/Ion1,4-BENZOQUINONE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
2MHO4Mod. Amino AcidS-OXYMETHIONINE
3PLQ4Ligand/Ion1,4-BENZOQUINONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:9 , MHO A:10 , TYR A:11 , GLY A:12 , HIS A:13 , ILE A:14 , PRO A:76 , THR A:77 , ARG A:78 , PHE A:79 , GLY A:80 , SER A:112 , THR A:113 , GLY A:114 , THR A:115 , GLY A:116 , GLY A:117 , HOH A:328 , HOH A:329 , ASP B:91 , HIS B:132 , PLQ B:201binding site for residue FMN A 201
2AC2SOFTWARETRP A:97 , HIS A:132 , TYR A:142 , PHE B:79 , FMN B:202binding site for residue PLQ A 202
3AC3SOFTWAREPHE A:79 , FMN A:201 , TRP B:97 , HIS B:132 , TYR B:142binding site for residue PLQ B 201
4AC4SOFTWAREASP A:91 , HIS A:132 , PLQ A:202 , SER B:9 , MHO B:10 , TYR B:11 , GLY B:12 , HIS B:13 , ILE B:14 , PRO B:76 , THR B:77 , ARG B:78 , PHE B:79 , GLY B:80 , SER B:112 , THR B:113 , GLY B:114 , THR B:115 , GLY B:116 , GLY B:117 , HOH B:304 , HOH B:312binding site for residue FMN B 202
5AC5SOFTWARETYR A:8 , SER A:9 , GLY A:12 , HIS A:13 , PHE A:47 , ALA A:50 , GLY A:51 , GLY A:52 , LYS A:53 , ARG A:78 , FMN A:201 , HOH A:331 , HOH A:340 , HOH A:341 , HOH A:370 , HOH A:388binding site for Ligand residues MHO A 10 through TYR A 11 bound to SER A 9
6AC6SOFTWARETYR B:8 , SER B:9 , GLY B:12 , HIS B:13 , MET B:42 , PHE B:47 , ALA B:50 , GLY B:51 , GLY B:52 , LYS B:53 , ARG B:78 , FMN B:202 , HOH B:336binding site for Ligand residues MHO B 10 through TYR B 11 bound to SER B 9

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YQE)

(-) 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:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhh...........hhhhhhh.eeeeeee......hhhhhhhhh.hhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhh..ee.............eee.........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yqe A   1 AKVLVLYYSmYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  ||   161       171       181       191      
                                    10-MHO                                                                                                                              143|                                          
                                                                                                                                                                         155                                          


Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhh...........hhhhhhh.eeeeeee......hhhhhhhhh.hhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhh..ee......hhhhh......................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yqe B   1 AKVLVLYYSmYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 ||    163       173       183       193    
                                    10-MHO                                                                                                                                       152|                                         
                                                                                                                                                                                  156
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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 4YQE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NQOR_ECOLI | P0A8G6: 2r96 2r97 2rg1 3b6i 3b6j 3b6k 3b6m 3zho 5f12

(-) Related Entries Specified in the PDB File

2r96 WRBA IN COMPLEX WITH FMN
2r97 WRBA IN COMPLEX WITH FMN
2rg1 WRBA APOPROTEIN
3zho WRBA IN COMPLEX WITH FMN AT 1.2 A RESOLUTION