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(-) Description

Title :  THE CRYSTALLOGRAPHIC STRUCTURE OF FLAVORUBREDOXIN FROM ESCHERICHIA COLI
 
Authors :  C. V. Romao, J. B. Vicente, T. Bandeiras, M. A. Carrondo, M. Teixeira, C.
Date :  23 Apr 14  (Deposition) - 03 Sep 14  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Electron Transport, Fdp, Nitric Oxide, Roo, Rubredoxin, Flrd (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. V. Romao, J. B. Vicente, P. T. Borges, B. L. Victor, P. Lamosa, E. Silva, T. M. Bandeiras, C. M. Soares, M. A. Carrondo, D. Turner, M. Teixeira, C. Frazao
Structure Of Escherichia Coli Flavodiiron Nitric Oxide Reductase.
J. Mol. Biol. V. 428 4686 2016
PubMed-ID: 27725182  |  Reference-DOI: 10.1016/J.JMB.2016.10.008

(-) Compounds

Molecule 1 - ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Expression System Vector: PET24
    Expression System Vector Type: PLASMID
    Fragment: B-LACTAMASE FLAVODOXIN DOMAIN, RESIDUES 1-479
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synonym: FLRD, FLAVORB, FLAVORUBREDOXIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric Unit (6, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FE2Ligand/IonFE (III) ION
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
4GOL2Ligand/IonGLYCEROL
5O1Ligand/IonOXYGEN ATOM
6PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE-1Ligand/IonFE (III) ION
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
4GOL4Ligand/IonGLYCEROL
5O-1Ligand/IonOXYGEN ATOM
6PO44Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:23 , GLU A:81 , TRP A:148 , THR A:260 , MET A:261 , SER A:262 , ASN A:263 , ASN A:264 , THR A:265 , SER A:313 , THR A:314 , MET A:315 , ASN A:316 , ASN A:317 , SER A:345 , HIS A:346 , GLY A:347 , TRP A:348 , SER A:349 , GLY A:350 , TRP A:375 , HOH A:2299 , HOH A:2300 , HOH A:2338BINDING SITE FOR RESIDUE FMN A 482
02AC2SOFTWAREASP A:83 , HIS A:84 , ASP A:166 , HIS A:227 , FE A:603 , O A:604 , PO4 A:605BINDING SITE FOR RESIDUE FE A 602
03AC3SOFTWAREHIS A:79 , GLU A:81 , HIS A:147 , ASP A:166 , FE A:602 , O A:604 , PO4 A:605BINDING SITE FOR RESIDUE FE A 603
04AC4SOFTWAREHIS A:79 , GLU A:81 , ASP A:83 , HIS A:84 , ASP A:166 , FE A:602 , FE A:603 , PO4 A:605BINDING SITE FOR RESIDUE O A 604
05AC5SOFTWAREPHE A:22 , HIS A:23 , GLU A:81 , ASP A:83 , HIS A:147 , ASP A:166 , HIS A:171 , HIS A:227 , FE A:602 , FE A:603 , O A:604 , HOH A:2239BINDING SITE FOR RESIDUE PO4 A 605
06AC6SOFTWAREASP A:68 , ALA A:70 , ASP A:71 , ASP A:73 , HOH A:2112 , HOH A:2115 , HOH A:2116BINDING SITE FOR RESIDUE PO4 A 606
07AC7SOFTWAREARG A:193 , THR A:300BINDING SITE FOR RESIDUE CL A 607
08AC8SOFTWAREGLY A:351 , HOH A:2365 , HOH A:2370BINDING SITE FOR RESIDUE CL A 608
09AC9SOFTWAREGLN A:184 , PHE A:188 , GLN A:237 , HOH A:2228 , HOH A:2423BINDING SITE FOR RESIDUE GOL A 609
10BC1SOFTWAREARG A:31 , GLU A:186 , ARG A:304 , HOH A:2234 , HOH A:2237 , HOH A:2331BINDING SITE FOR RESIDUE GOL A 610

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D02)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:146 -His A:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D02)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FLAVODOXIN_LIKEPS50902 Flavodoxin-like domain profile.NORV_ECOLI254-393  1A:254-393
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FLAVODOXIN_LIKEPS50902 Flavodoxin-like domain profile.NORV_ECOLI254-393  2A:254-393

(-) Exons   (0, 0)

(no "Exon" information available for 4D02)

(-) 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:399
 aligned with NORV_ECOLI | Q46877 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:399
                                    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       381       391         
           NORV_ECOLI     2 SIVVKNNIHWVGQRDWEVRDFHGTEYKTLRGSSYNSYLIREEKNVLIDTVDHKFSREFVQNLRNEIDLADIDYIVINHAEEDHAGALTELMAQIPDTPIYCTANAIDSINGHHHHPEWNFNVVKTGDTLDIGNGKQLIFVETPMLHWPDSMMTYLTGDAVLFSNDAFGQHYCDEHLFNDEVDQTELFEQCQRYYANILTPFSRLVTPKITEILGFNLPVDMIATSHGVVWRDNPTQIVELYLKWAADYQEDRITIFYDTMSNNTRMMADAIAQGIAETDPRVAVKIFNVARSDKNEILTNVFRSKGVLVGTSTMNNVMMPKIAGLVEEMTGLRFRNKRASAFGSHGWSGGAVDRLSTRLQDAGFEMSLSLKAKWRPDQDALKLCREHGREIARQWALAP 400
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee..eee....ee....ee....eee..eeee...eeee...hhhhhhhhhhhhhhhhhhhhh.eee..........hhhhhhhhh....eeehhhhhhhhhhhhh.....eee.....eeeee..eeeeeee.........eeeee....eeeee.............hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......eeee....ee...hhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhheeeeeee........hhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhh..ee...eeee...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FLAVODOXIN_LIKE  PDB: A:254-393 UniProt: 254-393                                                                                            ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d02 A   2 SIVVKNNIHWVGQRDWEVRDFHGTEYKTLRGSSYNSYLIREEKNVLIDTVDHKFSREFVQNLRNEIDLADIDYIVINHAEEDHAGALTELMAQIPDTPIYCTANAIDSINGHHHHPEWNFNVVKTGDTLDIGNGKQLIFVETPMLHWPDSMMTYLTGDAVLFSNDAFGQHYCDEHLFNDEVDQTELFEQCQRYYANILTPFSRLVTPKITEILGFNLPVDMIATSHGVVWRDNPTQIVELYLKWAADYQEDRITIFYDTMSNNTRMMADAIAQGIAETDPRVAVKIFNVARSDKNEILTNVFRSKGVLVGTSTMNNVMMPKIAGLVEEMTGLRFRNKRASAFGSHGWSGGAVDRLSTRLQDAGFEMSLSLKAKWRPDQDALKLCREHGREIARQWALAP 400
                                    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       381       391
   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 4D02)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D02)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D02)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (NORV_ECOLI | Q46877)
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:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016966    nitric oxide reductase activity    Catalysis of the reaction: H(2)O + 2 ferricytochrome c + nitrous oxide = 2 H(+) + 2 ferrocytochrome c + 2 nitric oxide.
    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.
    GO:0016661    oxidoreductase activity, acting on other nitrogenous compounds as donors    Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0046210    nitric oxide catabolic process    The chemical reactions and pathways resulting in the breakdown of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
    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:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0071731    response to nitric oxide    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 a nitric oxide stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  4d02
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 Related Entries

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UniProtKB/Swiss-Prot
        NORV_ECOLI | Q46877: 2ms3 5lld 5lmc

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