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(-) Description

Title :  CRYSTAL STRUCTURE OF NA(+)-TRANSLOCATING NADH-QUINONE REDUCTASE SUBUNIT C (YP_001302508.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.10 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  24 Feb 10  (Deposition) - 31 Mar 10  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Na(+)-Translocating Nadh-Quinone Reductase Subunit C, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transport, Ubiquinone, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Na(+)-Translocating Nadh-Quinone Reductase Subunit C (Yp_001302508. 1) From Parabacteroides Distasonis Atcc 8503 At 1. 10 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 73-270
    Gene: BDI_1123
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:156 , TRP A:166 , HOH A:295 , HOH A:302 , HOH A:330 , HOH A:403 , HOH A:551 , HOH A:592 , HOH A:609BINDING SITE FOR RESIDUE GOL A 271
2AC2SOFTWARELYS A:107 , GLU A:110 , ASP A:178 , LYS A:179 , ASN A:180 , PHE A:215 , LEU A:266 , THR A:267 , HOH A:292 , HOH A:327 , HOH A:329 , HOH A:473 , HOH A:522 , HOH A:586BINDING SITE FOR RESIDUE GOL A 272
3AC3SOFTWAREGLN A:235 , ASP A:252 , PHE A:256 , HOH A:301 , HOH A:308 , HOH A:411 , HOH A:418BINDING SITE FOR RESIDUE GOL A 273

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LWX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LWX)

(-) 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:199
 aligned with A6LB22_PARD8 | A6LB22 from UniProtKB/TrEMBL  Length:270

    Alignment length:199
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
         A6LB22_PARD8    72 SQSLRSFQKQNEDNDKRQQILRSINVNVSSSEAETKYNELIKEAFLVNENGEKVEGDAFATDVVKAATEHQYPVFVANVDGQPKYIMALHGAGLWGPLWGYISVDSDKNTIYGADFSHQGETPGLGAEISKPVFSNEFKGKKIFMSGEFKSVAVVKPGKSVAGQDYVDGISGGTITSKGVDEMLFNSLSGYVKFLTSQN 270
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------FMN_bind-3lwxA01 A:164-262                                                                         -------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhheeeeeeee....ee.......hhhhhhhh.eeeeeeeee..eeeeeeeeeee....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh....ee..ee...eee..........eee....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwx A   0 GQSLRSFQKQNEDNDKRQQILRSINVNVSSSEAETKYNELIKEAFLVNENGEKVEGDAFATDVVKAATEHQYPVFVANVDGQPKYImALHGAGLWGPLWGYISVDSDKNTIYGADFSHQGETPGLGAEISKPVFSNEFKGKKIFmSGEFKSVAVVKPGKSVAGQDYVDGISGGTITSKGVDEmLFNSLSGYVKFLTSQN 270
                            ||      81        91       101       111       121       131       141       151      |161       171       181       191       201       211    |  221       231       241       251  |    261         
                            ||                                                                                  158-MSE                                                   216-MSE                               254-MSE            
                            0|                                                                                                                                                                                                     
                            73
   Legend:   → Mismatch (orange background)
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  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 3LWX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: FMN_bind] (2)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A6LB22_PARD8 | A6LB22)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0006814    sodium ion transport    The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009276    Gram-negative-bacterium-type cell wall    The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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