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(-) Description

Title :  CRYSTAL STRUCTURE OF AZOREDUCTASE AZRC FIN COMPLEX WITH SULFONE-MODIFIED AZO DYE ACID RED 88
 
Authors :  J. Yu, D. Ogata, T. Ooi, M. Yao
Date :  27 Feb 13  (Deposition) - 12 Feb 14  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Azoreductase, Azo Bond Cleavage, Fmn-Binding, Azoreductase- Azoreductase Substrate Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Yu, D. Ogata, Z. Gai, S. Taguchi, I. Tanaka, T. Ooi, M. Yao
Structures Of Azra And Of Azrc Complexed With Substrate Or Inhibitor: Insight Into Substrate Specificity And Catalytic Mechanism
Acta Crystallogr. , Sect. D V. 70 553 2014
PubMed: search  |  Reference-DOI: 10.1107/S1399004713030988

(-) Compounds

Molecule 1 - FMN-DEPENDENT NADH-AZOREDUCTASE
    Chains: A, B, C, D
    EC Number: 1.7.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AZRC, AZOR
    Organism Scientific: BACILLUS
    Organism Taxid: 391699
    Strain: B29
    Synonym: AZO-DYE REDUCTASE, FMN-DEPENDENT NADH-AZO COMPOUND OXIDOREDUCTASE

 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  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
3K4Ligand/IonPOTASSIUM ION
4RE84Ligand/Ion4-[(E)-(2-HYDROXYNAPHTHALEN-1-YL)DIAZENYL]NAPHTHALENE-1-SULFONIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3K-1Ligand/IonPOTASSIUM ION
4RE82Ligand/Ion4-[(E)-(2-HYDROXYNAPHTHALEN-1-YL)DIAZENYL]NAPHTHALENE-1-SULFONIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3K-1Ligand/IonPOTASSIUM ION
4RE82Ligand/Ion4-[(E)-(2-HYDROXYNAPHTHALEN-1-YL)DIAZENYL]NAPHTHALENE-1-SULFONIC ACID

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:10 , SER A:17 , PHE A:18 , GLY A:19 , PRO A:101 , MET A:102 , TRP A:103 , ASN A:104 , PHE A:105 , ALA A:146 , THR A:147 , GLY A:148 , GLY A:149 , TYR A:151 , MET A:186 , ASN A:187 , RE8 A:302 , HOH A:404 , HOH A:430 , HOH A:450 , HOH A:451BINDING SITE FOR RESIDUE FMN A 301
02AC2SOFTWARETYR A:151 , ASN A:187 , FMN A:301 , HOH A:457 , PHE B:125 , TYR B:127 , PHE B:172BINDING SITE FOR RESIDUE RE8 A 302
03AC3SOFTWAREPHE A:125 , TYR A:127 , PHE A:172 , ASN B:104 , ASN B:187 , FMN B:301BINDING SITE FOR RESIDUE RE8 A 303
04AC4SOFTWAREASN A:203 , HOH A:439 , HOH A:459BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREGLU A:24 , GLU A:28 , HOH A:464 , GLU C:24BINDING SITE FOR RESIDUE K A 305
06AC6SOFTWAREILE A:52 , RE8 A:303 , ASN B:10 , SER B:17 , PHE B:18 , GLY B:19 , PRO B:101 , MET B:102 , TRP B:103 , ASN B:104 , PHE B:105 , ALA B:146 , THR B:147 , GLY B:148 , GLY B:149 , TYR B:151 , MET B:186 , ASN B:187 , HOH B:409 , HOH B:438BINDING SITE FOR RESIDUE FMN B 301
07AC7SOFTWARETHR B:8 , ALA B:9 , ASN B:10 , ASP B:43BINDING SITE FOR RESIDUE K B 302
08AC8SOFTWAREASN C:10 , SER C:17 , PHE C:18 , GLY C:19 , PRO C:101 , MET C:102 , TRP C:103 , ASN C:104 , PHE C:105 , ALA C:146 , THR C:147 , GLY C:148 , GLY C:149 , TYR C:151 , MET C:186 , ASN C:187 , RE8 C:302 , HOH C:402 , HOH C:434 , HOH C:437BINDING SITE FOR RESIDUE FMN C 301
09AC9SOFTWAREASN C:104 , PHE C:105 , TYR C:151 , ASN C:187 , FMN C:301 , HOH C:437 , PHE D:125 , TYR D:127 , PRO D:132 , PHE D:172BINDING SITE FOR RESIDUE RE8 C 302
10BC1SOFTWAREPHE C:125 , TYR C:127 , PRO C:132 , PHE C:172 , TYR D:151 , ASN D:187 , FMN D:301BINDING SITE FOR RESIDUE RE8 C 303
11BC2SOFTWAREASN C:203 , HOH C:452 , HOH C:460 , HOH C:468 , HOH C:470BINDING SITE FOR RESIDUE CA C 304
12BC3SOFTWARETHR C:8 , ASN C:10 , ASP C:43 , HOH C:431BINDING SITE FOR RESIDUE K C 305
13BC4SOFTWAREVAL C:39 , HOH C:405 , HOH C:450 , HOH C:458 , HOH C:471 , HOH C:472BINDING SITE FOR RESIDUE CA C 306
14BC5SOFTWAREGLU A:24 , HOH A:442 , GLU C:24 , GLU C:28BINDING SITE FOR RESIDUE K C 307
15BC6SOFTWARERE8 C:303 , ASN D:10 , SER D:17 , PHE D:18 , GLY D:19 , PRO D:101 , MET D:102 , TRP D:103 , ASN D:104 , PHE D:105 , ALA D:146 , THR D:147 , GLY D:148 , GLY D:149 , TYR D:151 , MET D:186 , ASN D:187 , HOH D:413 , HOH D:418BINDING SITE FOR RESIDUE FMN D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W7A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W7A)

(-) Exons   (0, 0)

(no "Exon" information available for 3W7A)

(-) 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:210
 aligned with C0STY1_9BACI | C0STY1 from UniProtKB/TrEMBL  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
         C0STY1_9BACI     2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhhhhhhhhh...eeeeee.hhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....ee......ee.....eeeeeeee......hhhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w7a A   2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211


Chain B from PDB  Type:PROTEIN  Length:210
 aligned with C0STY1_9BACI | C0STY1 from UniProtKB/TrEMBL  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
         C0STY1_9BACI     2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhhhhhhhhh...eeeeee.hhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....ee......ee.....eeeeeeee......hhhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w7a B   2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211


Chain C from PDB  Type:PROTEIN  Length:210
 aligned with C0STY1_9BACI | C0STY1 from UniProtKB/TrEMBL  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
         C0STY1_9BACI     2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhhhhhhhhh...eeeeee.hhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....ee......ee.....eeeeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w7a C   2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211


Chain D from PDB  Type:PROTEIN  Length:210
 aligned with C0STY1_9BACI | C0STY1 from UniProtKB/TrEMBL  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
         C0STY1_9BACI     2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....ee......ee.....eeeeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w7a D   2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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  (0, 0)

(no "SCOP Domain" information available for 3W7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W7A)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (C0STY1_9BACI | C0STY1)
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:0008752    FMN reductase activity    Catalysis of the reaction: FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    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.
    GO:0016652    oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    GO:0016661    oxidoreductase activity, acting on other nitrogenous compounds as donors    Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
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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  3w7a
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 Related Entries

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

UniProtKB/TrEMBL
        C0STY1_9BACI | C0STY1: 3w78 3w79

(-) Related Entries Specified in the PDB File

3w77 3w78 3w79