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(-) Description

Title :  CRYSTAL STRUCTURE OF NADH:RUBREDOXIN OXIDOREDUCTASE FROM CLOSTRIDIUM ACETOBUTYLICUM
 
Authors :  K. Nishikawa, Y. Shomura, S. Kawasaki, Y. Niimura, Y. Higuchi
Date :  08 Nov 09  (Deposition) - 16 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Fad-Binding Protein, Gr-Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Nishikawa, Y. Shomura, S. Kawasaki, Y. Niimura, Y. Higuchi
Crystal Structure Of Nadh:Rubredoxin Oxidoreductase From Clostridium Acetobutylicum: A Key Component Of The Dioxygen Scavenging System In Obligatory Anaerobes.
Proteins V. 78 1066 2010
PubMed-ID: 20017214  |  Reference-DOI: 10.1002/PROT.22650

(-) Compounds

Molecule 1 - NAD(FAD)-DEPENDENT DEHYDROGENASE, NIRB-FAMILY (N-TERMINAL DOMAIN)
    Chains: A
    EC Number: 1.18.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET7BLUE, PNROR
    Expression System Strain: TUNER(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NROR, CA_C2448
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid: 1488
    Synonym: NADH-RUBREDOXIN OXIDOREDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:9 , GLY A:10 , GLY A:12 , PRO A:13 , ALA A:14 , ASN A:33 , SER A:34 , GLU A:35 , ARG A:42 , PRO A:43 , GLU A:77 , PHE A:78 , ALA A:79 , ALA A:105 , SER A:106 , GLY A:107 , SER A:108 , TYR A:125 , LEU A:151 , ASN A:226 , PHE A:229 , GLY A:258 , ASP A:259 , GLY A:269 , LEU A:270 , ILE A:271 , ALA A:274 , LYS A:302 , HOH A:380 , HOH A:391 , HOH A:400 , HOH A:458BINDING SITE FOR RESIDUE FAD A 401

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:286

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:300 -Leu A:301

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KLJ)

(-) 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:378
 aligned with NROR_CLOAB | Q9AL95 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:378
                                    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        
           NROR_CLOAB     2 KSTKILILGAGPAGFSAAKAALGKCDDITMINSEKYLPYYRPRLNEIIAKNKSIDDILIKKNDWYEKNNIKVITSEFATSIDPNNKLVTLKSGEKIKYEKLIIASGSIANKIKVPHADEIFSLYSYDDALKIKDECKNKGKAFIIGGGILGIELAQAIIDSGTPASIGIILEYPLERQLDRDGGLFLKDKLDRLGIKIYTNSNFEEMGDLIRSSCVITAVGVKPNLDFIKDTEIASKRGILVNDHMETSIKDIYACGDVAEFYGKNPGLINIANKQGEVAGLNACGEDASYSEIIPSPILKVSGISIISCGDIENNKPSKVFRSTQEDKYIVCMLKENKIDAAAVIGDVSLGTKLKKAIDSSKSFDNISSLDAILNNL 379
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-3kljA01 A:142-218                                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---Pyr_redox_2-3kljA02 A:5-265                                                                                                                                                                                                                                          ------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ....eeee..hhhhhhhhhhhh.....eeee........hhhhhhhhhhh..hhhhh...hhhhhhhh..eee....eeeee....eeee....eee..eeee...eee..........ee...hhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhh...eee...hhhhhhhhhhhheeee...eee.hhhhh.........eee..........eee....eee......hhhhhhhhhhhhhhhhh.............eeee..eeeeee.........eeeeee....eeeeeee..eeeeeeee.hhhhhhhhhhhhhh........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3klj A   2 KSTKILILGAGPAGFSAAKAALGKCDDITMINSEKYLPYYRPRLNEIIAKNKSIDDILIKKNDWYEKNNIKVITSEFATSIDPNNKLVTLKSGEKIKYEKLIIASGSIANKIKVPHADEIFSLYSYDDALKIKDECKNKGKAFIIGGGILGIELAQAIIDSGTPASIGIILEYPLERQLDRDGGLFLKDKLDRLGIKIYTNSNFEEMGDLIRSSCVITAVGVKPNLDFIKDTEIASKRGILVNDHMETSIKDIYACGDVAEFYGKNPGLINIANKQGEVAGLNACGEDASYSEIIPSPILKVSGISIISCGDIENNKPSKVFRSTQEDKYIVCMLKENKIDAAAVIGDVSLGTKLKKAIDSSKSFDNISSLDAILNNL 379
                                    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
   Legend:   → Mismatch (orange background)
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  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 3KLJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NROR_CLOAB | Q9AL95)
molecular function
    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: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: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:0015044    rubredoxin-NAD+ reductase activity    Catalysis of the reaction: reduced rubredoxin + NAD+ = oxidized rubredoxin + NADH + H+.
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.
    GO:0072592    oxygen metabolic process    The chemical reactions and pathways involving diatomic oxygen (O2).
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.

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