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(-) Description

Title :  NADH:QUINONE OXIDOREDUCTASE (NDH-II) FROM STAPHYLOCOCCUS AUREUS - HOLOPROTEIN STRUCTURE
 
Authors :  J. A. Brito, A. L. Rosario, F. V. Sena, A. P. Batista, T. O. Oliveira, M. M. M. Archer
Date :  19 Dec 14  (Deposition) - 04 Nov 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.32
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alternative Nadh Dehydrogenase, Staphylococcus Aureus, Fad, Quinone, Quinol, Allostery, Protein-Substrate Interaction, Oxidoreductase, Membrane Protein, Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. V. Sena, A. P. Batista, T. Catarino, J. A. Brito, M. Archer, M. Viertler, T. Madl, E. J. Cabrita, M. M. Pereira
Type-Ii Nadh:Quinone Oxidoreductase From Staphylococcus Aureus Has Two Distinct Binding Sites And Is Rate Limited B Quinone Reduction.
Mol. Microbiol. V. 98 272 2015
PubMed-ID: 26172206  |  Reference-DOI: 10.1111/MMI.13120

(-) Compounds

Molecule 1 - NADH DEHYDROGENASE-LIKE PROTEIN SAOUHSC_00878
    Chains: A, B, C, D
    EC Number: 1.6.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA 2 (DE3)PLYSS
    Expression System Taxid: 562
    Gene: SAOUHSC_00878
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325
    Organism Taxid: 93061

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:12 , GLY A:14 , TYR A:15 , ALA A:16 , ASN A:39 , LYS A:40 , ASN A:41 , TYR A:45 , ALA A:47 , THR A:48 , HIS A:51 , ALA A:81 , GLU A:82 , VAL A:83 , LEU A:109 , GLY A:110 , PHE A:111 , ILE A:128 , PHE A:168 , THR A:169 , GLU A:172 , LEU A:270 , GLY A:301 , ASP A:302 , THR A:317 , THR A:318 , ALA A:319 , GLN A:320 , LYS A:379binding site for residue FAD A 1001
02AC2SOFTWAREGLY B:14 , TYR B:15 , ALA B:16 , ASN B:39 , LYS B:40 , ASN B:41 , TYR B:45 , ALA B:47 , THR B:48 , HIS B:51 , VAL B:83 , LEU B:109 , GLY B:110 , PHE B:111 , ILE B:128 , PHE B:168 , GLU B:172 , LEU B:270 , GLY B:301 , ASP B:302 , THR B:318 , ALA B:319 , LYS B:379binding site for residue FAD B 1001
03AC3SOFTWAREARG B:88 , GLU B:276binding site for residue CL B 1002
04AC4SOFTWARETYR B:45binding site for residue CL B 1003
05AC5SOFTWAREGLY C:12 , GLY C:14 , TYR C:15 , ALA C:16 , ASN C:39 , LYS C:40 , ASN C:41 , TYR C:45 , ALA C:47 , THR C:48 , ALA C:81 , GLU C:82 , VAL C:83 , LEU C:109 , GLY C:110 , PHE C:111 , PHE C:168 , GLU C:172 , LEU C:270 , GLY C:301 , ASP C:302 , THR C:317 , THR C:318 , ALA C:319 , GLN C:320 , LYS C:379binding site for residue FAD C 1001
06AC6SOFTWAREGLU C:201 , ALA C:202 , ILE C:235binding site for residue CL C 1002
07AC7SOFTWAREGLU C:142binding site for residue CL C 1003
08AC8SOFTWAREGLU C:114 , THR C:115 , LYS C:122binding site for residue CL C 1004
09AC9SOFTWAREGLY D:12 , GLY D:14 , TYR D:15 , ALA D:16 , ASN D:39 , LYS D:40 , ASN D:41 , TYR D:45 , ALA D:47 , THR D:48 , ALA D:81 , GLU D:82 , VAL D:83 , LEU D:109 , GLY D:110 , PHE D:111 , PHE D:168 , LEU D:270 , GLY D:301 , ASP D:302 , THR D:317 , THR D:318 , ALA D:319 , GLN D:320binding site for residue FAD D 1001
10AD1SOFTWAREARG D:139binding site for residue CL D 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XDB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu C:153 -Lys C:154
2Glu D:153 -Lys D:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XDB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XDB)

(-) Exons   (0, 0)

(no "Exon" information available for 4XDB)

(-) 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 A from PDB  Type:PROTEIN  Length:400
                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhh....eeeeeee...eee...hhhhhhh........eee.hhhh....eeeee..eeeee....eeee..eeee..eeee...eee............ee..hhhhhhhhhhhhhhhhhhhhhh...hhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhheeeee..........hhhhhhhhhhhhhhh.eeee....eeee....eeeee..eeee....eeee...eee.hhhhhhh..ee..ee......ee..eeeeee.hhhh.............hhhhhhhhhhhhhhhhhhhhh............eeeeee...eeeeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdb A   3 QDRKKVLVLGAGYAGLQTVTKLQKAISTEEAEITLINKNEYHYEATWLHEASAGTLNYEDVLYPVESVLKKDKVNFVQAEVTKIDRDAKKVETNQGIYDFDILVVALGFVSETFGIEGMKDHAFQIENVITARELSRHIEDKFANYAASKEKDDNDLSILVGGAGFTGVEFLGELTDRIPELCSKYGVDQNKVKITCVEAAPKMLPMFSEELVNHAVSYLEDRGVEFKIATPIVACNEKGFVVEVDGEKQQLNAGTSVWAAGVRGSKLMEESFEGVKRGRIVTKQDLTINGYDNIFVIGDCSAFIPAGEERPLPTTAQIAMQQGESVAKNIKRILNGESTEEFEYVDRGTVCSLGSHDGVGMVFGKPIAGKKAAFMKKVIDTRAVFKIGGIGLAFKKGKF 402
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402


Chain B from PDB  Type:PROTEIN  Length:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh.....eeeeee...eee...hhhhhhhh.......eee.hhhh....eeeee..eeeee....eeee..eeee..eeee...eee......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhheeeeee.........hhhhhhhhhhhhhhh.eeeee...eeee....eeeee..eeee....eeee...eee.hhhhhhh..ee..ee.............eee.hhhh.............hhhhhhhhhhhhhhhhhhhhh............eeeee.....eeeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdb B   4 DRKKVLVLGAGYAGLQTVTKLQKAISTEEAEITLINKNEYHYEATWLHEASAGTLNYEDVLYPVESVLKKDKVNFVQAEVTKIDRDAKKVETNQGIYDFDILVVALGFVSETFGIEGMKDHAFQIENVITARELSRHIEDKFANYAASKEKDDNDLSILVGGAGFTGVEFLGELTDRIPELCSKYGVDQNKVKITCVEAAPKMLPMFSEELVNHAVSYLEDRGVEFKIATPIVACNEKGFVVEVDGEKQQLNAGTSVWAAGVRGSKLMEESFEGVKRGRIVTKQDLTINGYDNIFVIGDCSAFIPAGEERPLPTTAQIAMQQGESVAKNIKRILNGESTEEFEYVDRGTVCSLGSHDGVGMVFGKPIAGKKAAFMKKVIDTRAVFKIGGIGLAFKKGKF 402
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393         


Chain C from PDB  Type:PROTEIN  Length:398
                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh....eeeeeee...eee...hhhhhhhh.......eee.hhhh....eeeee..eeeee....eeee..eeee..eeee...eee......hhhhhhee..hhhhhhhhhhhhhhhhhhhh.....hhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhheeeee..........hhhhhhhhhhhhhh..eeee....eeee....eeeee..eeee....eeee...eee.hhhhhhh..ee..ee......ee..eeeeee.hhhh.............hhhhhhhhhhhhhhhhhhhhh............eeeee.....eeeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdb C   5 RKKVLVLGAGYAGLQTVTKLQKAISTEEAEITLINKNEYHYEATWLHEASAGTLNYEDVLYPVESVLKKDKVNFVQAEVTKIDRDAKKVETNQGIYDFDILVVALGFVSETFGIEGMKDHAFQIENVITARELSRHIEDKFANYAASKEKDDNDLSILVGGAGFTGVEFLGELTDRIPELCSKYGVDQNKVKITCVEAAPKMLPMFSEELVNHAVSYLEDRGVEFKIATPIVACNEKGFVVEVDGEKQQLNAGTSVWAAGVRGSKLMEESFEGVKRGRIVTKQDLTINGYDNIFVIGDCSAFIPAGEERPLPTTAQIAMQQGESVAKNIKRILNGESTEEFEYVDRGTVCSLGSHDGVGMVFGKPIAGKKAAFMKKVIDTRAVFKIGGIGLAFKKGKF 402
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394        


Chain D from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh.....eeeeee...eee...hhhhhhhh.......eee.hhhh....eeeee..eeeee....eeee..eeee..eeee...eee......hhhhhhee..hhhhhhhhhhhhhhhhhhhhh....hhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhheeeee..........hhhhhhhhhhhhhh..eeee....eeee....eeeee..eeee....eeee...eee.hhhhhhh..ee..ee......ee..eeeeee.hhhh.............hhhhhhhhhhhhhhhhhhhhh............eeeee.....eeeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdb D   6 KKVLVLGAGYAGLQTVTKLQKAISTEEAEITLINKNEYHYEATWLHEASAGTLNYEDVLYPVESVLKKDKVNFVQAEVTKIDRDAKKVETNQGIYDFDILVVALGFVSETFGIEGMKDHAFQIENVITARELSRHIEDKFANYAASKEKDDNDLSILVGGAGFTGVEFLGELTDRIPELCSKYGVDQNKVKITCVEAAPKMLPMFSEELVNHAVSYLEDRGVEFKIATPIVACNEKGFVVEVDGEKQQLNAGTSVWAAGVRGSKLMEESFEGVKRGRIVTKQDLTINGYDNIFVIGDCSAFIPAGEERPLPTTAQIAMQQGESVAKNIKRILNGESTEEFEYVDRGTVCSLGSHDGVGMVFGKPIAGKKAAFMKKVIDTRAVFKIGGIGLAFKKGKF 402
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395
   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 4XDB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XDB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XDB)

(-) Gene Ontology  (2, 2)

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