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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI WRBA IN COMPLEX WITH FMN
 
Authors :  I. Kuta Smatanova, J. Wolfova, J. Brynda, J. R. Mesters, R. Grandori, J. Carey
Date :  12 Sep 07  (Deposition) - 23 Sep 08  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Electron Transport, Quinone Oxidoreductase, Flavoprotein, Flavodoxin-Like Fold, Fmn-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wolfova, I. K. Smatanova, J. Brynda, J. R. Mesters, M. Lapkouski, M. Kuty, A. Natalello, N. Chatterjee, S. Y. Chern, E. Ebbel, A. Ricci, R. Grandori, R. Ettrich, J. Carey
Structural Organization Of Wrba In Apo- And Holoprotein Crystals.
Biochim. Biophys. Acta V. 1794 1288 2009
PubMed-ID: 19665595  |  Reference-DOI: 10.1016/J.BBAPAP.2009.08.001
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FLAVOPROTEIN WRBA
    Chains: A, C
    EC Number: 1.6.5.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKGWA
    Expression System Strain: CY15071(LAMBDA-DE3)
    Expression System Vector Type: PLASMID
    Gene: WRBA
    Organism Scientific: ESCHERICHIA COLI
    Other Details: GENOMIC SEQUENCE CLONED IN PET3A
    Strain: K-12/JM101
    Synonym: TRP REPRESSOR-BINDING PROTEIN A

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1EDO14Ligand/Ion1,2-ETHANEDIOL
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (2, 32)
No.NameCountTypeFull Name
1EDO28Ligand/Ion1,2-ETHANEDIOL
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:9 , MET 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 , SER A:112 , THR A:113 , GLY A:114 , GLY A:116 , GLY A:117 , TYR A:142 , EDO A:204 , HOH A:208 , HOH A:224 , ASP C:91 , HIS C:132 , EDO C:204BINDING SITE FOR RESIDUE FMN A 198
02AC2SOFTWAREALA A:143 , ALA A:144 , GLN A:145 , GLU A:146BINDING SITE FOR RESIDUE EDO A 199
03AC3SOFTWARETHR A:41 , GLY A:84 , GLN A:85 , HOH A:231 , THR C:88 , ASP C:91BINDING SITE FOR RESIDUE EDO A 200
04AC4SOFTWARELEU A:191 , LYS A:194 , GLU C:48BINDING SITE FOR RESIDUE EDO A 201
05AC5SOFTWAREARG A:37 , GLU A:40 , THR A:54 , GLN A:55BINDING SITE FOR RESIDUE EDO A 202
06AC6SOFTWARETRP A:97 , HOH A:247 , FMN C:198 , EDO C:199BINDING SITE FOR RESIDUE EDO A 203
07AC7SOFTWAREGLY A:114 , THR A:115 , FMN A:198 , TRP C:97 , EDO C:204BINDING SITE FOR RESIDUE EDO A 204
08AC8SOFTWAREALA A:22 , SER A:26 , VAL A:33BINDING SITE FOR RESIDUE EDO A 205
09AC9SOFTWARETYR A:183 , GLU A:186 , TYR A:187 , HOH A:239BINDING SITE FOR RESIDUE EDO A 206
10BC1SOFTWAREASP A:91 , HIS A:132 , EDO A:203 , SER C:9 , MET C:10 , TYR C:11 , GLY C:12 , HIS C:13 , ILE C:14 , PRO C:76 , THR C:77 , ARG C:78 , PHE C:79 , SER C:112 , THR C:113 , GLY C:114 , THR C:115 , GLY C:117 , TYR C:142 , EDO C:199 , HOH C:214 , HOH C:232BINDING SITE FOR RESIDUE FMN C 198
11BC2SOFTWAREEDO A:203 , GLY C:114 , THR C:115 , FMN C:198BINDING SITE FOR RESIDUE EDO C 199
12BC3SOFTWARELYS C:2 , GLU C:32 , ASP C:67BINDING SITE FOR RESIDUE EDO C 200
13BC4SOFTWARETYR C:7 , TYR C:8 , SER C:9 , ARG C:37 , VAL C:38 , GLN C:55BINDING SITE FOR RESIDUE EDO C 201
14BC5SOFTWARETYR C:11 , GLY C:12 , HIS C:13 , THR C:16 , GLN C:172 , PRO C:173BINDING SITE FOR RESIDUE EDO C 202
15BC6SOFTWAREARG C:171 , GLN C:172BINDING SITE FOR RESIDUE EDO C 203
16BC7SOFTWAREFMN A:198 , EDO A:204 , TRP C:97 , HOH C:242BINDING SITE FOR RESIDUE EDO C 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R96)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Gly A:51 -Gly A:52
2Gly A:52 -Lys A:53
3Gly A:114 -Thr A:115
4Asn A:196 -Gly A:197
5Ala C:50 -Gly C:51
6Gly C:51 -Gly C:52
7Gly C:52 -Lys C:53
8Gly C:114 -Thr C:115
9Asn C:196 -Gly C:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R96)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FLAVODOXIN_LIKEPS50902 Flavodoxin-like domain profile.NQOR_ECOLI4-189
 		  2A:3-188
C:3-188
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FLAVODOXIN_LIKEPS50902 Flavodoxin-like domain profile.NQOR_ECOLI4-189
 		  4A:3-188
C:3-188

(-) Exons   (0, 0)

(no "Exon" information available for 2R96)

(-) 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:197
 aligned with NQOR_ECOLI | P0A8G6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           NQOR_ECOLI     2 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 198
               SCOP domains d2r96a_ A: Trp repressor binding protein WrbA                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhh..........hhhhhhh.eeeeeee......hhhhhhhhh.hhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhh..ee......hhhhhh............eee.........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FLAVODOXIN_LIKE  PDB: A:3-188 UniProt: 4-189                                                                                                                                              --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r96 A   1 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       


Chain C from PDB  Type:PROTEIN  Length:197
 aligned with NQOR_ECOLI | P0A8G6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           NQOR_ECOLI     2 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 198
               SCOP domains d2r96c_ C: Trp repressor binding protein WrbA                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhh...........hhhhhhhh.eeeeeee......hhhhhhhhh.hhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhh..ee......hhhhhh............eee.........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FLAVODOXIN_LIKE  PDB: C:3-188 UniProt: 4-189                                                                                                                                              --------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r96 C   1 AKVLVLYYSMYGHIETMARAVAEGASKVDGAEVVVKRVPETMPPQLFEKAGGKTQTAPVATPQELADYDAIIFGTPTRFGNMSGQMRTFLDQTGGLWASGALYGKLASVFSSTGTGGGQEQTITSTWTTLAHHGMVIVPIGYAAQELFDVSQVRGGTPYGATTIAGGDGSRQPSQEELSIARYQGEYVAGLAVKLNG 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R96)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R96)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (NQOR_ECOLI | P0A8G6)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0003955    NAD(P)H dehydrogenase (quinone) activity    Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  2r96
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 Related Entries

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

UniProtKB/Swiss-Prot
        NQOR_ECOLI | P0A8G6: 2r97 2rg1 3b6i 3b6j 3b6k 3b6m 3zho 4yqe 5f12

(-) Related Entries Specified in the PDB File

2r97 E. COLI WRBA IN COMPLEX WITH OXIDIZED FMN, CRYSTAL FORM GROWN FROM 20% PEG 8000, 0.1M TRIS-HCL, PH 8.0
2rg1 E. COLI WRBA APOPROTEIN