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(-) Description

Title :  CRYSTAL STRUCTURE OF REDUCED YQJM FROM BACILLUS SUBTILIS
 
Authors :  K. Kitzing, T. B. Fitzpatrick, C. Wilken, J. Sawa, G. P. Bourenkov, P. Macheroux, T. Clausen
Date :  15 Mar 05  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Flavin, Fmn, Beta-Alpha-Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Kitzing, T. B. Fitzpatrick, C. Wilken, J. Sawa, G. P. Bourenkov, P. Macheroux, T. Clausen
The 1. 3 A Crystal Structure Of The Flavoprotein Yqjm Reveals A Novel Class Of Old Yellow Enzymes
J. Biol. Chem. V. 280 27904 2005
PubMed-ID: 15890652  |  Reference-DOI: 10.1074/JBC.M502587200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE NADH-DEPENDENT FLAVIN OXIDOREDUCTASE YQJM
    ChainsA, B
    EC Number1.-.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL21-CODON-PLUS(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymYQJM

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric Unit (2, 22)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 44)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
2MSE40Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:23 , PRO A:24 , MSE A:25 , CYS A:26 , ALA A:60 , GLN A:102 , HIS A:164 , HIS A:167 , ARG A:215 , VAL A:283 , MSE A:285 , GLY A:307 , ARG A:308 , HOH A:1503 , HOH A:1512 , HOH A:1514 , HOH A:1533 , HOH A:1558 , HOH A:1567BINDING SITE FOR RESIDUE FMN A 1500
2AC2SOFTWAREARG A:336 , SER B:23 , PRO B:24 , MSE B:25 , CYS B:26 , ALA B:60 , GLN B:102 , HIS B:164 , HIS B:167 , ARG B:215 , VAL B:283 , GLY B:284 , MSE B:285 , GLY B:307 , ARG B:308 , HOH B:1509 , HOH B:1529 , HOH B:1539 , HOH B:1559 , HOH B:1565 , HOH B:1593BINDING SITE FOR RESIDUE FMN B 1501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z48)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z48)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z48)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z48)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z48)

(-) 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:337
 aligned with NAMA_BACSU | P54550 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
           NAMA_BACSU     2 ARKLFTPITIKDMTLKNRIVMSPMCMYSSHEKDGKLTPFHMAHYISRAIGQVGLIIVEASAVNPQGRITDQDLGIWSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGRKAELEGDIFAPSAIAFDEQSATPVEMSAEKVKETVQEFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVKQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWMKEQGVDLIDCSSGALVHADINVFPGYQVSFAEKIREQADMATGAVGMITDGSMAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW 338
               SCOP domains d1z48a_ A: NADPH dehydrogenase NamA                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eee..eee...eee...............hhhhhhhhhhhhhh...eeeeeeee.hhhhh.....ee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh......ee.............ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhh.eeee.....hhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhh......hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z48 A   2 ARKLFTPITIKDmTLKNRIVmSPmCmYSSHEKDGKLTPFHmAHYISRAIGQVGLIIVEASAVNPQGRITDQDLGIWSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGRKAELEGDIFAPSAIAFDEQSATPVEmSAEKVKETVQEFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVKQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWmKEQGVDLIDCSSGALVHADINVFPGYQVSFAEKIREQADmATGAVGmITDGSmAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW 338
                                    11  |     21|  | |  31        41|       51        61        71        81        91       101       111       121       131  |    141       151       161       171       181       191       201       211       221       231      |241       251       261       271      |281   |   291       301       311       321       331       
                                       14-MSE  22-MSE|             42-MSE                                                                                     134-MSE                                                                                                 238-MSE                                 278-MSE  |     |                                               
                                                  25-MSE                                                                                                                                                                                                                                                             285-MSE |                                               
                                                    27-MSE                                                                                                                                                                                                                                                                 291-MSE                                           

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with NAMA_BACSU | P54550 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
           NAMA_BACSU     2 ARKLFTPITIKDMTLKNRIVMSPMCMYSSHEKDGKLTPFHMAHYISRAIGQVGLIIVEASAVNPQGRITDQDLGIWSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGRKAELEGDIFAPSAIAFDEQSATPVEMSAEKVKETVQEFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVKQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWMKEQGVDLIDCSSGALVHADINVFPGYQVSFAEKIREQADMATGAVGMITDGSMAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW 338
               SCOP domains d1z48b_ B: NADPH dehydrogenase NamA                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Oxidored_FMN-1z48B01 B:4-327                                                                                                                                                                                                                                                                                                        ----------- Pfam domains (1)
           Pfam domains (2) --Oxidored_FMN-1z48B02 B:4-327                                                                                                                                                                                                                                                                                                        ----------- Pfam domains (2)
         Sec.struct. author .hhhhh.eee..eee...eee...............hhhhhhhhhhhhhh...eeeeeeee.hhhhh.....ee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh......ee.............ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhhhhhh..eee.....hhhhhhhhhhh....eeee.hhhhhh.hhhhhhhhhh......hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z48 B   2 ARKLFTPITIKDmTLKNRIVmSPmCmYSSHEKDGKLTPFHmAHYISRAIGQVGLIIVEASAVNPQGRITDQDLGIWSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGRKAELEGDIFAPSAIAFDEQSATPVEmSAEKVKETVQEFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVKQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWmKEQGVDLIDCSSGALVHADINVFPGYQVSFAEKIREQADmATGAVGmITDGSmAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW 338
                                    11  |     21|  | |  31        41|       51        61        71        81        91       101       111       121       131  |    141       151       161       171       181       191       201       211       221       231      |241       251       261       271      |281   |   291       301       311       321       331       
                                       14-MSE  22-MSE|             42-MSE                                                                                     134-MSE                                                                                                 238-MSE                                 278-MSE  |     |                                               
                                                  25-MSE                                                                                                                                                                                                                                                             285-MSE |                                               
                                                    27-MSE                                                                                                                                                                                                                                                                 291-MSE                                           

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z48)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NAMA_BACSU | P54550)
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:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0003959    NADPH dehydrogenase activity    Catalysis of the reaction: NADPH + H+ + acceptor = NADP+ + reduced acceptor.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0018548    pentaerythritol trinitrate reductase activity    Catalysis of the reaction: pentaerythritol trinitrate + NADPH = NADP+ + nitrate + pentaerythritol dinitrate.
    GO:0052690    trichloro-p-hydroquinone reductive dehalogenase activity    Catalysis of the reaction: 2,3,6-trichlorohydroquinone + 2 glutathione = 2,6-dichlorohydroquinone + glutathione disulfide + HCl.
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:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NAMA_BACSU | P545501z41 1z42 1z44

(-) Related Entries Specified in the PDB File

1z41 OXIDIZED YQJM
1z42 OXIDIZED YQJM COMPLEXED WITH P-HYDROXYBENZALDEHYDE
1z44 OXIDIZED YQJM COMPLEXED WITH P-NITROPHENOL