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(-) Description

Title :  YLR011WP, A SACCHAROMYCES CEREVISIAE NA(D)PH-DEPENDENT FMN REDUCTASE
 
Authors :  D. Liger, M. Graille, C. -Z. Zhou, N. Leulliot, S. Quevillon-Cheruel, K. Blondeau, J. Janin, H. Van Tilbeurgh
Date :  09 Apr 04  (Deposition) - 22 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Saccharomyces Cerevisiae, Fmn Binding Protein, Flavodoxin, Azoreductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Liger, M. Graille, C. -Z. Zhou, N. Leulliot, S. Quevillon-Cheruel, K. Blondeau, J. Janin, H. Van Tilbeurgh
Crystal Structure And Functional Characterization Of Yeast Ylr011Wp, An Enzyme With Nad(P)H-Fmn And Ferric Iron Reductase Activities
J. Biol. Chem. V. 279 34890 2004
PubMed-ID: 15184374  |  Reference-DOI: 10.1074/JBC.M405404200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YLR011WP
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 9
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YLR011W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:134 , GLU A:138 , HOH A:260BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREASP A:134 , GLU A:138 , HOH A:218 , HOH A:219 , HOH A:226BINDING SITE FOR RESIDUE CA A 202
3AC3SOFTWARESER A:9 , ARG A:11 , ARG A:14 , VAL A:15 , CYS A:16 , PRO A:93 , GLN A:94 , TYR A:95 , ASN A:96 , TRP A:97 , TYR A:124 , GLY A:126 , VAL A:157 , HOH A:208 , HOH A:216 , HOH A:244 , HOH A:259 , ILE B:60 , ASP B:108BINDING SITE FOR RESIDUE FMN A 200
4AC4SOFTWAREILE A:60 , ASP A:108 , SER B:9 , ARG B:11 , ARG B:14 , VAL B:15 , CYS B:16 , PRO B:93 , GLN B:94 , TYR B:95 , ASN B:96 , TRP B:97 , TYR B:124 , GLY B:126 , VAL B:157 , HOH B:208 , HOH B:209 , HOH B:211 , HOH B:218BINDING SITE FOR RESIDUE FMN B 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T0I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:160 -Pro A:161
2Ile B:160 -Pro B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T0I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T0I)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR011W1YLR011W.1XII:169102-169677576LOT6_YEAST1-1911912A:1-185
B:2-186 (gaps)		185
185

(-) 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:185
 aligned with LOT6_YEAST | Q07923 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
           LOT6_YEAST     1 MKVGIIMGSVRAKRVCPEIAAYVKRTIENSEELIDQKLKIQVVDLQQIALPLYEDDDELIPAQIKSVDEYADSKTRSWSRIVNALDIIVFVTPQYNWGYPAALKNAIDRLYHEWHGKPALVVSYGGHGGSKCNDQLQEVLHGLKMNVIGGVAVKIPVGTIPLPEDIVPQLSVHNEEILQLLASCI 185
               SCOP domains d1t0ia_ A: Hypothetical protein Ylr011wp                                                                                                                                                  SCOP domains
               CATH domains 1t0iA00 A:1-185  [code=3.40.50.360, no name defined]                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhh.........eeeeehhhhhh..........hhhhh.hhhhh.hhhhhhhhhhhhh..eeeeeee......hhhhhhhhhh........eeeeeeee...hhhhhhhhhhhhhhh..eeeeeeeee............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-185 UniProt: 1-191 [INCOMPLETE]                                                                                                                                        Transcript 1
                 1t0i A   1 MKVGIIMGSVRAKRVCPEIAAYVKRTIENSEELIDQKLKIQVVDLQQIALPLYEDDDELIPAQIKSVDEYADSKTRSWSRIVNALDIIVFVTPQYNWGYPAALKNAIDRLYHEWHGKPALVVSYGGHGGSKCNDQLQEVLHGLKMNVIGGVAVKIPVGTIPLPEDIVPQLSVHNEEILQLLASCI 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with LOT6_YEAST | Q07923 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
           LOT6_YEAST     2 KVGIIMGSVRAKRVCPEIAAYVKRTIENSEELIDQKLKIQVVDLQQIALPLYEDDDELIPAQIKSVDEYADSKTRSWSRIVNALDIIVFVTPQYNWGYPAALKNAIDRLYHEWHGKPALVVSYGGHGGSKCNDQLQEVLHGLKMNVIGGVAVKIPVGTIPLPEDIVPQLSVHNEEILQLLASCIE 186
               SCOP domains d1t0ib_ B: Hypothetical prote        in Ylr011wp                                                                                                                                          SCOP domains
               CATH domains 1t0iB00 B:2-186  [code=3.40.5        0.360, no name defined]                                                                                                                              CATH domains
           Pfam domains (1) FMN_red-1t0iB01 B:2-159                                                                                                                                       --------------------------- Pfam domains (1)
           Pfam domains (2) FMN_red-1t0iB02 B:2-159                                                                                                                                       --------------------------- Pfam domains (2)
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhh..--------.eeeeehhhhh..........hhhhh.hhhhh.hhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhh........eeeeeeee...hhhhhhhhhhhhhhh..eeeeeeeee............hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-186 (gaps) UniProt: 1-191 [INCOMPLETE]                                                                                                                                 Transcript 1
                 1t0i B   2 KVGIIMGSVRAKRVCPEIAAYVKRTIENS--------KIQVVDLQQIALPLYEDDDELIPAQIKSVDEYADSKTRSWSRIVNALDIIVFVTPQYNWGYPAALKNAIDRLYHEWHGKPALVVSYGGHGGSKCNDQLQEVLHGLKMNVIGGVAVKIPVGTIPLPEDIVPQLSVHNEEILQLLASCIE 186
                                    11        21        |-       |41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
                                                       30       39
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Flavoprotein (71)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LOT6_YEAST | Q07923)
molecular function
    GO:0052874    FMN reductase (NADH) activity    Catalysis of the reaction: FMNH2 + NAD+ = FMN + NADH + 2 H+.
    GO:0052873    FMN reductase (NADPH) activity    Catalysis of the reaction: FMNH2 + NADP+ = FMN + NADPH + 2 H+.
    GO:0003955    NAD(P)H dehydrogenase (quinone) activity    Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0034599    cellular response to oxidative stress    Any process that results in a change in state or activity of a cell (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.
    GO:0042994    cytoplasmic sequestering of transcription factor    The selective interaction of a transcription factor with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1nni BACILLUS SUBTILIS AZOBENZENE REDUCTASE