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(-) Description

Title :  L122Y MUTANT OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F)
 
Authors :  N. Shibata, Y. Higuchi
Date :  28 Jun 04  (Deposition) - 19 Jul 05  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Electron Transport, Flavoprotein, Fmn (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kitamura, K. Terakawa, H. Inoue, T. Hayashida, K. Suto, Y. Morimoto, N. Yasuoka, N. Shibata, Y. Higuchi
Determination Of The Role Of The Carboxyl-Terminal Leucine-122 In Fmn-Binding Protein By Mutational And Structural Analysis.
J. Biochem. V. 141 459 2007
PubMed-ID: 17261542  |  Reference-DOI: 10.1093/JB/MVM051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FMN-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'
    Organism Taxid: 883
    Strain: MIYAZAKI F

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:27 , VAL A:29 , ASN A:30 , THR A:31 , TRP A:32 , TYR A:35 , PRO A:47 , GLY A:49 , GLY A:50 , MET A:51 , HIS A:52 , LYS A:53 , THR A:54 , TRP A:106 , HOH A:1127 , HOH A:1223 , GLY B:82 , THR B:121 , TYR B:122 , HOH B:2162BINDING SITE FOR RESIDUE FMN A 1123
2AC2SOFTWAREGLY A:82 , THR A:121 , TYR A:122 , HOH A:1125 , HOH A:1169 , HIS B:27 , VAL B:29 , ASN B:30 , THR B:31 , TRP B:32 , TYR B:35 , PRO B:47 , GLY B:49 , GLY B:50 , MET B:51 , HIS B:52 , LYS B:53 , THR B:54 , HOH B:2124 , HOH B:2204 , HOH B:2209BINDING SITE FOR RESIDUE FMN B 2123

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WLI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WLI)

(-) Sequences/Alignments

Asymmetric/Biological 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:122
 aligned with FMNB_DESVM | Q46604 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
           FMNB_DESVM     1 MLPGTFFEVLKNEGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL 122
               SCOP domains d1wlia_ A: FMN-binding protein                                                                                             SCOP domains
               CATH domains 1wliA00 A:1-122 Electron Transport, Fmn-binding Protein; Chain A                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeeeeeee..eeeeeeee.hhheee...eeeeee..hhhhhhhhhhh.eeeeeeee..........eeeeeeeeeeee.hhhhhhh........eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wli A   1 MLPGTFFEVLKNEGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTY 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with FMNB_DESVM | Q46604 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
           FMNB_DESVM     1 MLPGTFFEVLKNEGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL 122
               SCOP domains d1wlib_ B: FMN-binding protein                                                                                             SCOP domains
               CATH domains 1wliB00 B:1-122 Electron Transport, Fmn-binding Protein; Chain A                                                           CATH domains
           Pfam domains (1) -Pyridox_oxidase-1wliB01 B:2-96                                                                 -------------------------- Pfam domains (1)
           Pfam domains (2) -Pyridox_oxidase-1wliB02 B:2-96                                                                 -------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhh....eeeeeee....eeeeeee.hhheee...eeeeee..hhhhhhhhhhh.eeeeeeee..........eeeeeeeeeeee.hhhhhhh........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wli B   1 MLPGTFFEVLKNEGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTY 122
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: FMN-binding (25)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FMNB_DESVM | Q46604)
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: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:0004733    pyridoxamine-phosphate oxidase activity    Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
biological process
    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:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        FMNB_DESVM | Q46604: 1axj 1flm 1wlk 2e83 3a20 3a6q 3a6r 3amf 3awh 3vy2 3vy5 3vya

(-) Related Entries Specified in the PDB File

1flm
1wlk L122E MUTANT
1wll L122K MUTANT