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(-) Description

Title :  STRUCTURE OF 2,6-DIHYDROXYPYRIDINE-3-HYDROXYLASE FROM ARTHROBACTER NICOTINOVORANS
 
Authors :  N. Treiber, G. E. Schulz
Date :  21 Feb 08  (Deposition) - 13 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Oxidoreductase, Aromatic Hydroxylase, Nicotine Degradation, Flavin Mono-Oxygenase, Fad-Dependent Hydroxylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Treiber, G. E. Schulz
Structure Of 2, 6-Dihydroxypyridine 3-Hydroxylase From A Nicotine-Degrading Pathway.
J. Mol. Biol. V. 379 94 2008
PubMed-ID: 18440023  |  Reference-DOI: 10.1016/J.JMB.2008.03.032

(-) Compounds

Molecule 1 - 2,6-DIHYDROXYPYRIDINE HYDROXYLASE
    Chains: A, B, C
    EC Number: 1.14.13.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: ARTHROBACTER NICOTINOVORANS
    Organism Taxid: 29320
    Synonym: 2,6-DIHYDROXYPYRIDINE-3-HYDROXYLASE, DHPH

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2FAD3Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL3Ligand/IonGLYCEROL
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL2Ligand/IonGLYCEROL
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL2Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:12 , SER A:14 , ILE A:15 , SER A:16 , TYR A:34 , GLU A:35 , ARG A:36 , LEU A:41 , ILE A:48 , VAL A:49 , LYS A:118 , CYS A:119 , LEU A:120 , ALA A:148 , ASP A:149 , GLY A:150 , VAL A:154 , ARG A:173 , GLN A:222 , GLY A:305 , ASP A:306 , ALA A:316 , ALA A:317 , GLY A:318 , GLY A:319 , ALA A:320 , GOL A:1396 , ACT A:1397 , HOH A:2065 , HOH A:2067 , HOH A:2187 , HOH A:2188 , HOH A:2189 , HOH A:2190 , HOH A:2191BINDING SITE FOR RESIDUE FAD A1395
2AC2SOFTWARETYR A:206 , GLN A:222 , TYR A:224 , PRO A:313 , FAD A:1395 , HOH A:2192BINDING SITE FOR RESIDUE GOL A1396
3AC3SOFTWAREPRO A:311 , ARG A:312 , PRO A:313 , ALA A:316 , ALA A:317 , GLY A:318 , TYR A:357 , FAD A:1395 , HOH A:2159BINDING SITE FOR RESIDUE ACT A1397
4AC4SOFTWAREVAL B:11 , GLY B:12 , SER B:14 , ILE B:15 , SER B:16 , TYR B:34 , GLU B:35 , ARG B:36 , LEU B:41 , ILE B:48 , VAL B:49 , LYS B:118 , CYS B:119 , LEU B:120 , ALA B:148 , ASP B:149 , GLY B:150 , VAL B:154 , GLN B:222 , ASP B:306 , ALA B:316 , ALA B:317 , GLY B:318 , GLY B:319 , ALA B:320 , GOL B:1390 , ACT B:1391 , HOH B:2034 , HOH B:2125 , HOH B:2126 , HOH B:2127BINDING SITE FOR RESIDUE FAD B1389
5AC5SOFTWARETYR B:206 , GLN B:222 , TYR B:224 , PRO B:313 , FAD B:1389 , HOH B:2110BINDING SITE FOR RESIDUE GOL B1390
6AC6SOFTWAREARG B:312 , PRO B:313 , ALA B:316 , ALA B:317 , GLY B:318 , TYR B:357 , FAD B:1389 , HOH B:2109BINDING SITE FOR RESIDUE ACT B1391
7AC7SOFTWAREVAL C:11 , GLY C:12 , SER C:14 , ILE C:15 , SER C:16 , TYR C:34 , GLU C:35 , ARG C:36 , LEU C:41 , ILE C:48 , VAL C:49 , LYS C:118 , CYS C:119 , LEU C:120 , ASP C:149 , GLY C:150 , VAL C:154 , GLN C:222 , GLY C:305 , ASP C:306 , ALA C:316 , ALA C:317 , GLY C:318 , GLY C:319 , ALA C:320 , GOL C:1390 , ACT C:1391 , HOH C:2022 , HOH C:2066 , HOH C:2067 , HOH C:2068BINDING SITE FOR RESIDUE FAD C1389
8AC8SOFTWARETYR C:206 , GLN C:222 , TYR C:224 , PRO C:313 , ALA C:316 , FAD C:1389 , HOH C:2033BINDING SITE FOR RESIDUE GOL C1390
9AC9SOFTWAREPRO C:311 , ARG C:312 , PRO C:313 , ALA C:316 , ALA C:317 , GLY C:318 , TYR C:357 , FAD C:1389 , HOH C:2056BINDING SITE FOR RESIDUE ACT C1391

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VOU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VOU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VOU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VOU)

(-) Exons   (0, 0)

(no "Exon" information available for 2VOU)

(-) 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:393
 aligned with DHPH_PAENI | Q93NG3 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:393
                                    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       341       351       361       371       381       391   
           DHPH_PAENI     2 SPTTDRIAVVGGSISGLTAALMLRDAGVDVDVYERSPQPLSGFGTGIVVQPELVHYLLEQGVELDSISVPSSSMEYVDALTGERVGSVPADWRFTSYDSIYGGLYELFGPERYHTSKCLVGLSQDSETVQMRFSDGTKAEANWVIGADGGASVVRKRLLGIEPTYAGYVTWRGVLQPGEVADDVWNYFNDKFTYGLLDDGHLIAYPIPGRENAESPRLNFQWYWNVAEGPDLDELMTDVRGIRLPTSVHNNSLNPHNLRQFHSKGESLFKPFRDLVLNASSPFVTVVADATVDRMVHGRVLLIGDAAVTPRPHAAAGGAKACDDARTLAEVFTKNHDLRGSLQSWETRQLQQGHAYLNKVKKMASRLQHGGSFEPGNPAFAFGLPKVDEPSVV 394
               SCOP domains d2voua1 A:2-163,A:292-394 Dihydroxypyridine hydroxylase DhpH                                                                                                      d2voua2 A:164-291 Dihydroxypyridine hydroxylase DhpH                                                                            d2voua1 A:2-163,A:292-394 Dihydroxypyridine hydroxylase DhpH                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh..eeeee............eee.hhhhhhhhhhh..hhhhh.....eeeeee.....eeeeee....eeehhhhhhhhhhhhh...ee....eeeeee....eeeee....eeee.eeee.....hhhhhhhhh...eeeeeeeeeeee.....hhhhhhhhh.eeeeeee..eeeeeeee.........eeeeeeeee...hhhhhhhh..........eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeeee......ee..eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vou A   2 SPTTDRIAVVGGSISGLTAALMLRDAGVDVDVYERSPQPLSGFGTGIVVQPELVHYLLEQGVELDSISVPSSSMEYVDALTGERVGSVPADWRFTSYDSIYGGLYELFGPERYHTSKCLVGLSQDSETVQMRFSDGTKAEANWVIGADGGASVVRKRLLGIEPTYAGYVTWRGVLQPGEVADDVWNYFNDKFTYGLLDDGHLIAYPIPGRENAESPRLNFQWYWNVAEGPDLDELMTDVRGIRLPTSVHNNSLNPHNLRQFHSKGESLFKPFRDLVLNASSPFVTVVADATVDRMVHGRVLLIGDAAVTPRPHAAAGGAKASDDARTLAEVFTKNHDLRGSLQSWETRQLQQGHAYLNKVKKMASRLQHGGSFEPGNPAFAFGLPKVDEPSVV 394
                                    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       341       351       361       371       381       391   


Chain B from PDB  Type:PROTEIN  Length:387
 aligned with DHPH_PAENI | Q93NG3 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:387
                                    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       341       351       361       371       381       
           DHPH_PAENI     2 SPTTDRIAVVGGSISGLTAALMLRDAGVDVDVYERSPQPLSGFGTGIVVQPELVHYLLEQGVELDSISVPSSSMEYVDALTGERVGSVPADWRFTSYDSIYGGLYELFGPERYHTSKCLVGLSQDSETVQMRFSDGTKAEANWVIGADGGASVVRKRLLGIEPTYAGYVTWRGVLQPGEVADDVWNYFNDKFTYGLLDDGHLIAYPIPGRENAESPRLNFQWYWNVAEGPDLDELMTDVRGIRLPTSVHNNSLNPHNLRQFHSKGESLFKPFRDLVLNASSPFVTVVADATVDRMVHGRVLLIGDAAVTPRPHAAAGGAKACDDARTLAEVFTKNHDLRGSLQSWETRQLQQGHAYLNKVKKMASRLQHGGSFEPGNPAFAFGLPKV 388
               SCOP domains d2voub1 B:2-163,B:292-388 Dihydroxypyridine hydroxylase DhpH                                                                                                      d2voub2 B:164-291 Dihydroxypyridine hydroxylase DhpH                                                                            d2voub1 B:2-163,B:292-388 Dihydroxypyridine hydroxylase DhpH                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh..eeeee............eee.hhhhhhhhhhh..hhhhh.....eeeeee.....eeeeee....eeehhhhhhhhhhhhh...ee....eeeeee....eeeee....eeee.eeee.....hhhhhhhhh...eeeeeeeeeeee.....hhhhhhhhh.eeeeeee..eeeeeeee.........eeeeeeeee...hhhhhhhh..........eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeeee......ee..eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vou B   2 SPTTDRIAVVGGSISGLTAALMLRDAGVDVDVYERSPQPLSGFGTGIVVQPELVHYLLEQGVELDSISVPSSSMEYVDALTGERVGSVPADWRFTSYDSIYGGLYELFGPERYHTSKCLVGLSQDSETVQMRFSDGTKAEANWVIGADGGASVVRKRLLGIEPTYAGYVTWRGVLQPGEVADDVWNYFNDKFTYGLLDDGHLIAYPIPGRENAESPRLNFQWYWNVAEGPDLDELMTDVRGIRLPTSVHNNSLNPHNLRQFHSKGESLFKPFRDLVLNASSPFVTVVADATVDRMVHGRVLLIGDAAVTPRPHAAAGGAKASDDARTLAEVFTKNHDLRGSLQSWETRQLQQGHAYLNKVKKMASRLQHGGSFEPGNPAFAFGLPKV 388
                                    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       341       351       361       371       381       


Chain C from PDB  Type:PROTEIN  Length:387
 aligned with DHPH_PAENI | Q93NG3 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:387
                                    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       341       351       361       371       381       
           DHPH_PAENI     2 SPTTDRIAVVGGSISGLTAALMLRDAGVDVDVYERSPQPLSGFGTGIVVQPELVHYLLEQGVELDSISVPSSSMEYVDALTGERVGSVPADWRFTSYDSIYGGLYELFGPERYHTSKCLVGLSQDSETVQMRFSDGTKAEANWVIGADGGASVVRKRLLGIEPTYAGYVTWRGVLQPGEVADDVWNYFNDKFTYGLLDDGHLIAYPIPGRENAESPRLNFQWYWNVAEGPDLDELMTDVRGIRLPTSVHNNSLNPHNLRQFHSKGESLFKPFRDLVLNASSPFVTVVADATVDRMVHGRVLLIGDAAVTPRPHAAAGGAKACDDARTLAEVFTKNHDLRGSLQSWETRQLQQGHAYLNKVKKMASRLQHGGSFEPGNPAFAFGLPKV 388
               SCOP domains d2vouc1 C:2-163,C:292-388 Dihydroxypyridine hydroxylase DhpH                                                                                                      d2vouc2 C:164-291 Dihydroxypyridine hydroxylase DhpH                                                                            d2vouc1 C:2-163,C:292-388 Dihydroxypyridine hydroxylase DhpH                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh..eeeee............eee.hhhhhhhhhhh..hhhhh.....eeeeee.....eeeeee....eeehhhhhhhhhhhhh...ee....eeeeee....eeeee....eeee.eeee.....hhhhhhhhh...eeeeeeeeeeee.....hhhhhhhhh.eeeeeee..eeeeeeee.........eeeeeeeee...hhhhhhhh..........eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeeee......ee..eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vou C   2 SPTTDRIAVVGGSISGLTAALMLRDAGVDVDVYERSPQPLSGFGTGIVVQPELVHYLLEQGVELDSISVPSSSMEYVDALTGERVGSVPADWRFTSYDSIYGGLYELFGPERYHTSKCLVGLSQDSETVQMRFSDGTKAEANWVIGADGGASVVRKRLLGIEPTYAGYVTWRGVLQPGEVADDVWNYFNDKFTYGLLDDGHLIAYPIPGRENAESPRLNFQWYWNVAEGPDLDELMTDVRGIRLPTSVHNNSLNPHNLRQFHSKGESLFKPFRDLVLNASSPFVTVVADATVDRMVHGRVLLIGDAAVTPRPHAAAGGAKASDDARTLAEVFTKNHDLRGSLQSWETRQLQQGHAYLNKVKKMASRLQHGGSFEPGNPAFAFGLPKV 388
                                    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       341       351       361       371       381
   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  (2, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VOU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VOU)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DHPH_PAENI | Q93NG3)
molecular function
    GO:0018663    2,6-dihydroxypyridine 3-monooxygenase activity    Catalysis of the reaction: 2,6-dihydroxypyridine + H(+) + NADH + O(2) = 2,3,6-trihydroxypyridine + H(2)O + NAD(+).
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0019608    nicotine catabolic process    The chemical reactions and pathways resulting in the breakdown of nicotine, (S)(-)-3-(1-methyl-2-pyrrolidinyl)pyridine.
    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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  2vou
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  DHPH_PAENI | Q93NG3
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