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(-) Description

Title :  E13R MUTANT OF FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F)
 
Authors :  S. Sato, T. Nakanishi, H. Inoue, M. Kitamura
Date :  19 Aug 10  (Deposition) - 05 Oct 11  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sato, T. Nakanishi, H. Inoue, M. Kitamura
Crystal Structure Of E13R Mutant Of Fmn-Binding Protein Fro Desulfovibrio Vulgaris (Miyazaki F)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FMN-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DVMF_2023
    Mutation: YES
    Organism Scientific: DESULFOVIBRIO VULGARIS
    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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:27 , VAL A:29 , ASN A:30 , THR A:31 , TRP A:32 , TYR A:35 , PRO A:47 , VAL A:48 , GLY A:49 , GLY A:50 , MET A:51 , HIS A:52 , LYS A:53 , THR A:54 , TRP A:106 , HOH A:1005 , HOH A:1014 , HOH A:1045 , HOH A:1105 , HOH A:1261 , GLY B:82 , THR B:121BINDING SITE FOR RESIDUE FMN A 123
2AC2SOFTWAREGLY A:82 , THR A:121 , 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 , TRP B:106 , HOH B:1010 , HOH B:1183 , HOH B:1188 , HOH B:1207BINDING SITE FOR RESIDUE FMN B 123
3AC3SOFTWAREARG A:13 , GLY A:14 , ASN A:33 , SER A:34 , ARG B:71BINDING SITE FOR RESIDUE CL A 2001
4AC4SOFTWAREARG A:71 , ARG B:13 , GLY B:14 , ASN B:33 , SER B:34BINDING SITE FOR RESIDUE CL B 2002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AMF)

(-) 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 d3amfa_ A: FMN-binding protein                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeeeeee....eeeeeee.hhheee...eeeeee..hhhhhhhhhhh.eeeeeeee..........eeeeeeeeeeee.hhhhhhh........eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3amf A   1 MLPGTFFEVLKNRGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL 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 d3amfb_ B: FMN-binding protein                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeeeeee....eeeeeee.hhhee....eeeeee..hhhhhhhhhhh.eeeeeeeeeeeee..eeeeeeeeeeeeeee.hhhhhhh........eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3amf B   1 MLPGTFFEVLKNRGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL 122
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 1wli 1wlk 2e83 3a20 3a6q 3a6r 3awh 3vy2 3vy5 3vya

(-) Related Entries Specified in the PDB File

1flm