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(-) Description

Title :  CRYSTAL STRUCTURE OF NADPH-DEPENDENT QUINONE OXIDOREDUCTASE QOR2 COMPLEXED WITH NADPH FROM ESCHERICHIA COLI
 
Authors :  I. K. Kim, H. S. Yim, M. K. Kim, D. W. Kim, Y. M. Kim, S. S. Cha, S. O. Kang
Date :  13 Nov 07  (Deposition) - 27 May 08  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Sandwich, Complex With Nadph, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. K. Kim, H. S. Yim, M. K. Kim, D. W. Kim, Y. M. Kim, S. S. Cha, S. O. Kang
Crystal Structure Of A New Type Of Nadph-Dependent Quinone Oxidoreductase (Qor2) From Escherichia Coli
J. Mol. Biol. V. 379 372 2008
PubMed-ID: 18455185  |  Reference-DOI: 10.1016/J.JMB.2008.04.003

(-) Compounds

Molecule 1 - UNCHARACTERIZED OXIDOREDUCTASE YTFG
    Chains: A
    EC Number: 1.6.5.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: STRAIN K12
    Synonym: HYPOTHETICAL PROTEIN YTFG, YTFG GENE PRODUCT, NADPH- DEPENDENT QUINONE OXIDOREDUCTASE

 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
1CU1Ligand/IonCOPPER (II) ION
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:13 , GLU A:17 , GLU A:276 , HIS A:280BINDING SITE FOR RESIDUE CU A 1001
2AC2SOFTWARESER A:18 , LYS A:21 , ALA A:176 , ARG A:180 , HIS A:269 , SO4 A:1003BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWARELYS A:21 , ALA A:172 , ASP A:173 , ALA A:176 , ILE A:267 , HIS A:269 , SO4 A:1002BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWAREGLY A:6 , THR A:8 , GLY A:9 , GLN A:10 , LEU A:11 , ARG A:33 , TYR A:53 , SER A:73 , SER A:74 , SER A:75 , GLN A:83 , ASN A:137 , GLY A:138 , TRP A:139 , TYR A:140 , ASN A:143 , ARG A:171 , HOH A:1011 , HOH A:1102 , HOH A:1227BINDING SITE FOR RESIDUE NDP A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZCV)

(-) 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:283
 aligned with QOR2_ECOLI | P39315 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:283
                                    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   
           QOR2_ECOLI     1 MIAITGATGQLGHYVIESLMKTVPASQIVAIVRNPAKAQALAAQGITVRQADYGDEAALTSALQGVEKLLLISSSEVGQRAPQHRNVINAAKAAGVKFIAYTSLLHADTSPLGLADEHIETEKMLADSGIVYTLLRNGWYSENYLASAPAALEHGVFIGAAGDGKIASATRADYAAAAARVISEAGHEGKVYELAGDSAWTLTQLAAELTKQSGKQVTYQNLSEADFAAALKSVGLPDGLADMLADSDVGASKGGLFDDSKTLSKLIGHPTTTLAESVSHLFN 283
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -NmrA-2zcvA01 A:2-221                                                                                                                                                                                                        -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...hhh.eeeee.hhhhhhhhhh...eeee....hhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh.eeee..........hhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zcv A   1 MIAITGATGQLGHYVIESLMKTVPASQIVAIVRNPAKAQALAAQGITVRQADYGDEAALTSALQGVEKLLLISSSEVGQRAPQHRNVINAAKAAGVKFIAYTSLLHADTSPLGLADEHIETEKMLADSGIVYTLLRNGWYSENYLASAPAALEHGVFIGAAGDGKIASATRADYAAAAARVISEAGHEGKVYELAGDSAWTLTQLAAELTKQSGKQVTYQNLSEADFAAALKSVGLPDGLADMLADSDVGASKGGLFDDSKTLSKLIGHPTTTLAESVSHLFN 283
                                    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
   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 2ZCV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (QOR2_ECOLI | P39315)
molecular function
    GO:0003955    NAD(P)H dehydrogenase (quinone) activity    Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a hydroquinone.
    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:0016655    oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  2zcv
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  QOR2_ECOLI | P39315
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  1.6.5.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        QOR2_ECOLI | P39315: 2zcu

(-) Related Entries Specified in the PDB File

2zcu