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(-) Description

Title :  NIKD, AN UNUSUAL AMINO ACID OXIDASE ESSENTIAL FOR NIKKOMYCIN BIOSYNTHESIS: OPEN FORM AT 1.9A RESOLUTION
 
Authors :  C. J. Carrell, R. C. Bruckner, D. Venci, G. Zhao, M. S. Jorns, F. S. Mathews
Date :  19 Jan 07  (Deposition) - 31 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Flavoprotein, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Carrell, R. C. Bruckner, D. Venci, G. Zhao, M. S. Jorns, F. S. Mathews
Nikd, An Unusual Amino Acid Oxidase Essential For Nikkomycin Biosynthesis: Structures Of Closed And Open Forms At 1. 15 And 1. 90 A Resolution
Structure V. 15 928 2007
PubMed-ID: 17697998  |  Reference-DOI: 10.1016/J.STR.2007.06.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NIKD PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDV101
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NIKD
    Organism Scientific: STREPTOMYCES TENDAE
    Organism Taxid: 1932
    Other Details: OPEN FORM
    Strain: TU501

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
16PC1Ligand/IonPYRIDINE-2-CARBOXYLIC ACID
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:10 , GLY A:11 , GLY A:13 , PRO A:14 , VAL A:15 , LEU A:33 , GLU A:34 , ARG A:35 , HIS A:36 , ASN A:40 , GLY A:43 , GLY A:44 , THR A:45 , ARG A:50 , HIS A:51 , THR A:175 , VAL A:176 , ALA A:203 , CYS A:204 , GLY A:205 , TYR A:207 , PHE A:260 , CYS A:321 , LEU A:322 , TYR A:351 , GLY A:354 , TRP A:355 , ALA A:356 , PHE A:357 , LYS A:358 , 6PC A:2001 , HOH A:3003 , HOH A:3025 , HOH A:3026 , HOH A:3036 , HOH A:3042 , HOH A:3163 , HOH A:3164BINDING SITE FOR RESIDUE FAD A 1001
2AC2SOFTWAREARG A:53 , GLU A:101 , PHE A:242 , TYR A:258 , TRP A:355 , FAD A:1001 , MPD A:3001 , HOH A:3064 , HOH A:3134BINDING SITE FOR RESIDUE 6PC A 2001
3AC3SOFTWAREASN A:100 , GLU A:101 , TRP A:355 , 6PC A:2001BINDING SITE FOR RESIDUE MPD A 3001
4AC4SOFTWAREASN A:100 , TYR A:224BINDING SITE FOR RESIDUE MPD A 3002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OLO)

(-) 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:393
 aligned with Q9X9P9_STRTE | Q9X9P9 from UniProtKB/TrEMBL  Length:389

    Alignment length:393
                                                                                                                                                                                                                                                                                                                                                                                                                             389     
                                    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       | -   
         Q9X9P9_STRTE     2 TESYDVVVVGGGPVGLATAWQVAERGHRVLVLERHTFFNENGGTSGAERHWRLQYTQEDLFRLTLETLPLWRALESRCERRLIHEIGSLWFGDTDVVTNEGQISGTAAMMDKLSVRYEWLKATDIERRFGFRGLPRDYEGFLQPDGGTIDVRGTLAALFTLAQAAGATLRAGETVTELVPDADGVSVTTDRGTYRAGKVVLACGPYTNDLLEPLGARLAYSVYEMAIAAYRQATPVTEAPFWFAFQQPTPQDTNLFYGFGHNPWAPGEFVRCGPDFEVDPLDHPSAATGVADRRQMDRLSGWLRDHLPTVDPDPVRTSTCLAVLPTDPERQFFLGTARDLMTHGEKLVVYGAGWAFKFVPLFGRICADLAVEDSTAYDISRLAPQSAL-----   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----DAO-2oloA01 A:6-370                                                                                                                                                                                                                                                                                                                                                          ------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhh...eeeee..............eeee.....hhhhhhhhhhhhhhhhhhhhhhh...eee..eeeee.........hhhhhhhhhhhhh...eeeehhhhhhhhh........eeeee...eeeehhhhhhhhhhhhhhh..eeee...eeeeeee..eeeeee...eeeeeeeee.hhhhhhhhhhhhh....eeeeeeeeeeee.........eeeee..........eee..........eeeeee........hhhhh....hhhhhhhhhhhhhhhh........eeeeeeeeee.......eeee......hhh.eeeeee..hhhhhhhhhhhhhhhhhhh.....hhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2olo A   2 TESYDVVVVGGGPVGLATAWQVAERGHRVLVLERHTFFNENGGTSGAERHWRLQYTQEDLFRLTLETLPLWRALESRCERRLIHEIGSLWFGDTDVVTNEGQISGTAAMMDKLSVRYEWLKATDIERRFGFRGLPRDYEGFLQPDGGTIDVRGTLAALFTLAQAAGATLRAGETVTELVPDADGVSVTTDRGTYRAGKVVLACGPYTNDLLEPLGARLAYSVYEMAIAAYRQATPVTEAPFWFAFQQPTPQDTNLFYGFGHNPWAPGEFVRCGPDFEVDPLDHPSAATGVADRRQMDRLSGWLRDHLPTVDPDPVRTSTCLAVLPTDPERQFFLGTARDLMTHGEKLVVYGAGWAFKFVPLFGRICADLAVEDSTAYDISRLAPQSALLEHHH 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
   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 2OLO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9X9P9_STRTE | Q9X9P9)
molecular function
    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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        Q9X9P9_STRTE | Q9X9P9: 2oln 2q6u 3hzl

(-) Related Entries Specified in the PDB File

2oln