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(-) Description

Title :  COMPLEX OF DITHIONITE-REDUCED 6-HYDROXY-L-NICOTINE OXIDASE WITH SUBSTRATE BOUND AT ACTIVE SITE AND INHIBITOR AT EXIT CAVITY
 
Authors :  G. S. Kachalova, H. D. Bartunik
Date :  11 Jun 10  (Deposition) - 16 Mar 11  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (2x)
Keywords :  Enantiomeric Substrate-Inhibitor, Flavoenzymes, Nicotine Degradation, Oxidase, Oxidoreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Kachalova, K. Decker, A. Holt, H. D. Bartunik
Crystallographic Snapshots Of The Complete Reaction Cycle O Nicotine Degradation By An Amine Oxidase Of The Monoamine Oxidase (Mao) Family
Proc. Natl. Acad. Sci. Usa V. 108 4800 2011
PubMed-ID: 21383134  |  Reference-DOI: 10.1073/PNAS.1016684108
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 6-HYDROXY-L-NICOTINE OXIDASE
    Chains: X
    EC Number: 1.5.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: JM105
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 6-HLNO
    Organism Scientific: ARTHROBACTER NICOTINOVORANS
    Organism Taxid: 29320

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (2x): X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GP71Ligand/Ion(1R)-2-{[(S)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTADECANOYLOXY)METHYL]ETHYL (12E)-HEXADECA-9,12-DIENOATE
3HNK1Ligand/Ion5-[(2R)-1-METHYLPYRROLIDIN-2-YL]PYRIDIN-2-OL
4HNL1Ligand/Ion5-[(2S)-1-METHYLPYRROLIDIN-2-YL]PYRIDIN-2-OL
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GP72Ligand/Ion(1R)-2-{[(S)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTADECANOYLOXY)METHYL]ETHYL (12E)-HEXADECA-9,12-DIENOATE
3HNK2Ligand/Ion5-[(2R)-1-METHYLPYRROLIDIN-2-YL]PYRIDIN-2-OL
4HNL2Ligand/Ion5-[(2S)-1-METHYLPYRROLIDIN-2-YL]PYRIDIN-2-OL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR X:59 , ASN X:166 , MET X:167 , LEU X:198 , TYR X:311 , PHE X:326 , GLY X:406 , TYR X:407 , FAD X:434BINDING SITE FOR RESIDUE HNL X 433
2AC2SOFTWAREGLY X:8 , GLY X:10 , PHE X:11 , SER X:12 , GLU X:31 , GLY X:32 , GLY X:37 , GLY X:38 , ARG X:39 , GLY X:56 , GLY X:57 , ALA X:58 , TYR X:59 , THR X:224 , VAL X:226 , ALA X:254 , THR X:255 , PRO X:256 , LYS X:287 , LEU X:366 , PHE X:367 , PRO X:370 , TRP X:371 , GLY X:397 , SER X:398 , GLY X:406 , TYR X:407 , ILE X:408 , HNL X:433 , HOH X:442 , HOH X:444 , HOH X:469 , HOH X:476 , HOH X:505 , HOH X:530 , HOH X:746 , HOH X:1008 , HOH X:1011BINDING SITE FOR RESIDUE FAD X 434
3AC3SOFTWAREVAL X:97 , ILE X:103 , PRO X:104 , GLY X:105 , THR X:115 , MET X:180 , LEU X:192 , HOH X:733 , HOH X:1120 , HOH X:1195BINDING SITE FOR RESIDUE GP7 X 435
4AC4SOFTWAREALA X:82 , SER X:83 , PHE X:85 , VAL X:195 , LEU X:198 , ASP X:312 , HOH X:660BINDING SITE FOR RESIDUE HNK X 436

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NG7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr X:266 -Pro X:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NG7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NG7)

(-) Exons   (0, 0)

(no "Exon" information available for 3NG7)

(-) 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 X from PDB  Type:PROTEIN  Length:427
 aligned with Q93NH4_PAENI | Q93NH4 from UniProtKB/TrEMBL  Length:425

    Alignment length:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  425  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420    |  
         Q93NH4_PAENI     1 MYDAIVVGGGFSGLKAARDLTNAGKKVLLLEGGERLGGRAYSRESRNVPGLRVEIGGAYLHRKHHPRLAAELDRYGIPTAAASEFTSFRHRLGPTAVDQAFPIPGSEAVAVEAATYTLLRDAHRIDLEKGLENQDLEDLDIPLNEYVDKLDLPPVSRQFLLAWAWNMLGQPADQASALWMLQLVAAHHYSILGVVLSLDEVFSNGSADLVDAMSQEIPEIRLQTVVTGIDQSGDVVNVTVKDGHAFQAHSVIVATPMNTWRRIVFTPALPERRRSVIEEGHGGQGLKILIHVRGAEAGIECVGDGIFPTLYDYCEVSESERLLVAFTDSGSFDPTDIGAVKDAVLYYLPEVEVLGIDYHDWIADPLFEGPWVAPRVGQFSRVHKELGEPAGRIHFVGSDVSLEFPGYIEGALETAECAVNAILHS--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh...eeee...........eee.......eee....ee....hhhhhhhhhhhh..eee.....ee...............hhhhhhhhhhhhhhhhhhhh............hhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhh..eee...hhhhhhhhhh....ee....eeeee.....eeeee.....eeeeeeee..hhhhhhhheee...hhhhhhhhhhh....eeeeeeeee.....eeee......eeeeeee....eeeeeeeee.......hhhhhhhhhhhhh...eeeeee.........................hhhhhh....eee.hhhhh.....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ng7 X   1 MYDAIVVGGGFSGLKAARDLTNAGKKVLLLEGGERLGGRAYSRESRNVPGLRVEIGGAYLHRKHHPRLAAELDRYGIPTAAASEFTSFRHRLGPTAVDQAFPIPGSEAVAVEAATYTLLRDAHRIDLEKGLENQDLEDLDIPLNEYVDKLDLPPVSRQFLLAWAWNMLGQPADQASALWMLQLVAAHHYSILGVVLSLDEVFSNGSADLVDAMSQEIPEIRLQTVVTGIDQSGDVVNVTVKDGHAFQAHSVIVATPMNTWRRIVFTPALPERRRSVIEEGHGGQGLKILIHVRGAEAGIECVGDGIFPTLYDYCEVSESERLLVAFTDSGSFDPTDIGAVKDAVLYYLPEVEVLGIDYHDWIADPLFEGPWVAPRVGQFSRVHKELGEPAGRIHFVGSDVSLEFPGYIEGALETAECAVNAILHSHH 427
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
   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 3NG7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NG7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NG7)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain X   (Q93NH4_PAENI | Q93NH4)
molecular function
    GO:0018531    (S)-6-hydroxynicotine oxidase activity    Catalysis of the reaction: (S)-6-hydroxynicotine + H(2)O + O(2) = 6-hydroxypseudooxynicotine + H(2)O(2).
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q93NH4_PAENI | Q93NH4: 3k7m 3k7q 3k7t 3ngc 3nh3 3nho 3nk0 3nk1 3nk2 3nn0 3nn6

(-) Related Entries Specified in the PDB File

3k7m APO FORM OF P432 SPACE GROUP
3k7q SUBSTRATE BOUND FORM OF P432 SPACE GROUP
3k7t APO FORM OF P3121 SPACE GROUP