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(-) Description

Title :  CRYSTAL STRUCTURE OF NADH:FMN OXIDOREDUCTASE LIKE PROTEIN IN COMPLEX WITH FMN (YP_544701.1) FROM METHYLOBACILLUS FLAGELLATUS KT AT 1.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  12 Aug 08  (Deposition) - 02 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Yp_544701. 1, Nadh:Fmn Oxidoreductase Like Protein In Complex With Fmn, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Nadh:Fmn Oxidoreductase Like Protein I Complex With Fmn (Yp_544701. 1) From Methylobacillus Flagellatus Kt At 1. 40 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_544701.1, MFLA_0590
    Organism Scientific: METHYLOBACILLUS FLAGELLATUS KT
    Organism Taxid: 265072

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 22)

Asymmetric/Biological Unit (6, 22)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3GOL4Ligand/IonGLYCEROL
4MSE12Mod. Amino AcidSELENOMETHIONINE
5NA2Ligand/IonSODIUM ION
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:32 , THR A:35 , GLY A:37 , PHE A:38 , ILE A:52 , ILE A:53 , GLY A:54 , TRP A:56 , ASP A:57 , TYR A:58 , SER A:59 , GLY A:86 , CYS A:88 , SER A:89 , GLY A:90 , LYS A:95 , HIS A:158 , HOH A:359 , LYS B:179 , TRP B:180 , HOH B:375BINDING SITE FOR RESIDUE FMN A 300
02AC2SOFTWARELYS A:179 , TRP A:180 , HOH A:321 , ASN B:32 , THR B:35 , GLY B:37 , PHE B:38 , ILE B:52 , ILE B:53 , GLY B:54 , TRP B:56 , ASP B:57 , TYR B:58 , SER B:59 , ILE B:85 , GLY B:86 , ASN B:87 , CYS B:88 , SER B:89 , GLY B:90 , LYS B:95 , HIS B:158 , HOH B:359BINDING SITE FOR RESIDUE FMN B 300
03AC3SOFTWAREGLU A:65 , THR A:66 , HOH A:322 , HOH A:362 , HOH A:504 , ASP B:110 , HOH B:332 , HOH B:436BINDING SITE FOR RESIDUE NA B 301
04AC4SOFTWAREHIS A:39 , HOH A:376 , HOH A:379 , HIS B:39 , HOH B:351 , HOH B:423BINDING SITE FOR RESIDUE NA A 301
05AC5SOFTWAREGLY A:174 , TRP A:180 , ARG A:181 , HOH A:495 , ASP B:161BINDING SITE FOR RESIDUE ACT A 302
06AC6SOFTWARETRP A:56 , TRP B:180 , HOH B:382BINDING SITE FOR RESIDUE GOL B 302
07AC7SOFTWAREHIS A:44 , TRP A:180 , HOH A:341 , TRP B:56BINDING SITE FOR RESIDUE GOL A 303
08AC8SOFTWAREPHE A:38 , ILE A:52 , TRP A:56 , GLN B:43 , HIS B:44 , HOH B:318 , HOH B:333BINDING SITE FOR RESIDUE GOL B 303
09AC9SOFTWAREHIS A:98 , HOH A:493 , HOH A:503 , GLN B:107BINDING SITE FOR RESIDUE GOL A 304
10BC1SOFTWAREALA A:92 , HOH A:493 , PRO B:105 , LEU B:113 , TRP B:145BINDING SITE FOR RESIDUE PEG A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E4V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:45 -Pro A:46
2Glu B:45 -Pro B:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E4V)

(-) Exons   (0, 0)

(no "Exon" information available for 3E4V)

(-) 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:179
 aligned with Q1H3S7_METFK | Q1H3S7 from UniProtKB/TrEMBL  Length:185

    Alignment length:179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172         
         Q1H3S7_METFK     3 NELPPENAYRILESGPIVLVSTRGADGRANLMTMGFHMMMQHEPPLVGAIIGPWDYSHQALSETGECVLAVPTVDLAETVVDIGNCSGDALDKFGHFGLTPVPAQTVDAPLVRQCWANLECRVVDDGWARRYNLWVLEVQRIWIDTARKETRLIHHQGDGRFSVDGDTLDLGERMTKWR 181
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh....eeeeee.....eeeeee..eeeee....eeeee.....hhhhhhhhhheeeeee.hhhhhhhhhhhh.......hhhhhhh..ee........ee....eeeeeeeee..hhhhhheeeeeeeeeee.........eee....eeeeeeeeee.hhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e4v A   3 NELPPENAYRILESGPIVLVSTRGADGRANLmTmGFHmmmQHEPPLVGAIIGPWDYSHQALSETGECVLAVPTVDLAETVVDIGNCSGDALDKFGHFGLTPVPAQTVDAPLVRQCWANLECRVVDDGWARRYNLWVLEVQRIWIDTARKETRLIHHQGDGRFSVDGDTLDLGERmTKWR 181
                                    12        22        32 | |   |42        52        62        72        82        92       102       112       122       132       142       152       162       172    |    
                                                          34-MSE |||                                                                                                                                    177-MSE
                                                            36-MSE||                                                                                                                                           
                                                                40-MSE                                                                                                                                         
                                                                 41-MSE                                                                                                                                        
                                                                  42-MSE                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:179
 aligned with Q1H3S7_METFK | Q1H3S7 from UniProtKB/TrEMBL  Length:185

    Alignment length:179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172         
         Q1H3S7_METFK     3 NELPPENAYRILESGPIVLVSTRGADGRANLMTMGFHMMMQHEPPLVGAIIGPWDYSHQALSETGECVLAVPTVDLAETVVDIGNCSGDALDKFGHFGLTPVPAQTVDAPLVRQCWANLECRVVDDGWARRYNLWVLEVQRIWIDTARKETRLIHHQGDGRFSVDGDTLDLGERMTKWR 181
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh....eeeeee.....eeeeee..eeeee....eeeee.....hhhhhhhhhheeeeee.hhhhhhhhhhhh.......hhhhhhh..ee........ee....eeeeeeeee..hhhhhheeeeeeeeeee.........eeeee..eeeeeeeeee.hhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e4v B   3 NELPPENAYRILESGPIVLVSTRGADGRANLmTmGFHmmmQHEPPLVGAIIGPWDYSHQALSETGECVLAVPTVDLAETVVDIGNCSGDALDKFGHFGLTPVPAQTVDAPLVRQCWANLECRVVDDGWARRYNLWVLEVQRIWIDTARKETRLIHHQGDGRFSVDGDTLDLGERmTKWR 181
                                    12        22        32 | |   |42        52        62        72        82        92       102       112       122       132       142       152       162       172    |    
                                                          34-MSE |||                                                                                                                                    177-MSE
                                                            36-MSE||                                                                                                                                           
                                                                40-MSE                                                                                                                                         
                                                                 41-MSE                                                                                                                                        
                                                                  42-MSE
   Legend:   → Mismatch (orange background)
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  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 3E4V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E4V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E4V)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q1H3S7_METFK | Q1H3S7)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
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.

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