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(-) Description

Title :  E13Q MUTANT OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F)
 
Authors :  T. Nakanishi, Y. Haruyama, H. Inoue, M. Kitamura
Date :  08 Sep 09  (Deposition) - 01 Sep 10  (Release) - 01 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Electron Transport, Flavoprotein, Fmn (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Chosrowjan, S. Taniguchi, N. Mataga, T. Nakanishi, Y. Haruyama, S. Sato, M. Kitamura, F. Tanaka
Effects Of The Disappearance Of One Charge On Ultrafast Fluorescence Dynamics Of The Fmn Binding Protein.
J. Phys. Chem. B V. 114 6175 2010
PubMed-ID: 20397678  |  Reference-DOI: 10.1021/JP912137S

(-) Compounds

Molecule 1 - FMN-BINDING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMKBT-1002
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DVMF_2023
    Mutation: YES
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 883
    Strain: MIYAZAKI F

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
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:1042 , HOH A:1288 , HOH A:1373 , HOH A:1457 , HOH A:1854 , GLY B:82 , THR B:121 , HOH B:1012BINDING SITE FOR RESIDUE FMN A 123
2AC2SOFTWAREGLN A:13 , GLY A:14 , ASN A:33 , SER A:34 , ARG B:71BINDING SITE FOR RESIDUE CL A 2002
3AC3SOFTWAREGLY A:82 , THR A:121 , HOH A:1047 , HIS B:27 , VAL B:29 , ASN B:30 , THR B:31 , TRP B:32 , TYR B:35 , PRO B:47 , VAL B:48 , GLY B:49 , GLY B:50 , MET B:51 , HIS B:52 , LYS B:53 , THR B:54 , TRP B:106 , HOH B:1023 , HOH B:1114 , HOH B:1293 , HOH B:1322 , HOH B:1383BINDING SITE FOR RESIDUE FMN B 123
4AC4SOFTWAREHIS C:27 , VAL C:29 , ASN C:30 , THR C:31 , TRP C:32 , TYR C:35 , PRO C:47 , GLY C:49 , GLY C:50 , MET C:51 , HIS C:52 , LYS C:53 , THR C:54 , TRP C:106 , HOH C:1052 , HOH C:1188 , HOH C:1282 , HOH C:1380 , GLY D:82 , THR D:121 , HOH D:1013BINDING SITE FOR RESIDUE FMN C 123
5AC5SOFTWAREGLN C:13 , GLY C:14 , ASN C:33 , SER C:34 , ARG D:71BINDING SITE FOR RESIDUE CL C 2001
6AC6SOFTWAREGLY C:82 , THR C:121 , HOH C:1043 , HIS D:27 , VAL D:29 , ASN D:30 , THR D:31 , TRP D:32 , TYR D:35 , PRO D:47 , GLY D:49 , GLY D:50 , MET D:51 , HIS D:52 , LYS D:53 , THR D:54 , HOH D:1028 , HOH D:1100 , HOH D:1159 , HOH D:1357 , HOH D:1625BINDING SITE FOR RESIDUE FMN D 123
7AC7SOFTWAREARG C:71 , GLN D:13 , GLY D:14 , ASN D:33 , SER D:34BINDING SITE FOR RESIDUE CL D 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A6R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A6R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A6R)

(-) Exons   (0, 0)

(no "Exon" information available for 3A6R)

(-) 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: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 d3a6ra_ A: FMN-binding protein                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh....eeeeeee....eeeeeee.hhheee...eeeeee..hhhhhhhhhhh.eeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhh........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a6r A   1 MLPGTFFEVLKNQGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL 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 d3a6rb_ B: FMN-binding protein                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeeeeeee..eeeeeeee.hhheee...eeeeee..hhhhhhhhhhh.eeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhh........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a6r B   1 MLPGTFFEVLKNQGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain C 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 d3a6rc_ C: FMN-binding protein                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeeeeee....eeeeeee.hhheee...eeeeee..hhhhhhhhhhh.eeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhh........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a6r C   1 MLPGTFFEVLKNQGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain D 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 d3a6rd_ D: FMN-binding protein                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeeeeee....eeeeeee.hhheee...eeeeee..hhhhhhhhhhh.eeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhh........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a6r D   1 MLPGTFFEVLKNQGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL 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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A6R)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 1wli 1wlk 2e83 3a20 3a6q 3amf 3awh 3vy2 3vy5 3vya

(-) Related Entries Specified in the PDB File

3a6q