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(-) Description

Title :  STRUCTURE OF THE SHEWANELLA LOIHICA PV-4 NADH-DEPENDENT PERSULFIDE REDUCTASE F161A MUTANT
 
Authors :  K. -H. Lee, M. H. Sazinsky, E. J. Crane
Date :  09 Jan 14  (Deposition) - 20 Aug 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Nadp-Dependant Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Lee, S. Humbarger, R. Bahnvadia, M. H. Sazinsky, E. J. Crane
Characterization Of The Mechanism Of The Nadh-Dependent Polysulfide Reductase (Npsr) From Shewanella Loihica Pv-4: Formation Of A Productive Nadh-Enzyme Complex And Its Role In The General Mechanism Of Nadh And Fad-Dependent Enzymes.
Biochim. Biophys. Acta V. 1844 1708 2014
PubMed-ID: 24981797  |  Reference-DOI: 10.1016/J.BBAPAP.2014.06.013

(-) Compounds

Molecule 1 - FAD-DEPENDENT PYRIDINE NUCLEOTIDE-DISULPHIDE OXIDOREDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SHEW_0729
    Mutation: YES
    Organism Scientific: SHEWANELLA LOIHICA
    Organism Taxid: 323850
    Strain: PV-4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1COA6Ligand/IonCOENZYME A
2FAD6Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:8 , VAL A:10 , ALA A:11 , GLY A:12 , PHE A:32 , GLU A:33 , ARG A:34 , ASN A:42 , CYS A:43 , HIS A:79 , GLU A:80 , VAL A:81 , SER A:112 , PRO A:113 , GLY A:114 , LEU A:133 , ARG A:134 , ILE A:162 , LEU A:271 , GLY A:302 , ASP A:303 , PRO A:319 , LEU A:320 , ALA A:321 , COA A:901 , HOH A:1004 , HOH A:1043 , HOH A:1066 , TYR B:446 , ALA B:447 , PRO B:448BINDING SITE FOR RESIDUE FAD A 900
2AC2SOFTWAREVAL A:10 , ALA A:11 , ALA A:14 , SER A:15 , ALA A:18 , ARG A:19 , ARG A:22 , SER A:39 , PHE A:40 , ASN A:42 , CYS A:43 , LEU A:61 , ALA A:321 , ASN A:325 , ARG A:329 , FAD A:900 , HOH A:1058 , HOH A:1080 , VAL B:380 , TYR B:446 , LYS B:454 , GLN B:459 , PHE B:462 , VAL B:463 , ASN B:466 , VAL B:533 , GLY B:534 , LEU B:535 , ASN B:538BINDING SITE FOR RESIDUE COA A 901
3AC3SOFTWARETYR A:446 , ALA A:447 , PRO A:448 , ILE B:7 , GLY B:8 , VAL B:10 , ALA B:11 , GLY B:12 , GLU B:33 , ARG B:34 , ASN B:42 , CYS B:43 , HIS B:79 , GLU B:80 , VAL B:81 , SER B:112 , PRO B:113 , GLY B:114 , LEU B:133 , ARG B:134 , ILE B:162 , LEU B:271 , GLY B:302 , ASP B:303 , PRO B:319 , LEU B:320 , ALA B:321 , ALA B:324 , COA B:901 , HOH B:1021 , HOH B:1031 , HOH B:1052 , HOH B:1080BINDING SITE FOR RESIDUE FAD B 900
4AC4SOFTWARETYR A:446 , LYS A:454 , GLN A:459 , PHE A:462 , VAL A:463 , ASN A:466 , VAL A:533 , GLY A:534 , LEU A:535 , ASN A:538 , HOH A:1050 , VAL B:10 , ALA B:11 , ALA B:14 , SER B:15 , ALA B:18 , ARG B:19 , ARG B:22 , SER B:39 , PHE B:40 , ASN B:42 , CYS B:43 , ASN B:325 , ARG B:329 , FAD B:900BINDING SITE FOR RESIDUE COA B 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met A:290 -Met A:291

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OCG)

(-) 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:565
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhh....hhhhhh..hhhhhhhhhh.eeee.eeeeeee....eeeeee.....eeeee..eeee...eee............ee...hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhh...eeee...eeeeeee......hhhhh..........eeeeee....eeee.eeee...eee.hhhhhhh......................eee.hhhh.ee......ee...hhhhhhhhhhhhhhhhh............eeeee..eeeeeee.hhhhhhh.....eeeeeeee..........eeeeeeee......eeeeeeee..hhhhhhhhhhhhhhh..hhhhhh..............hhhhhhhhhhhhhhh....ee...........eeeee..hhhhhhhh.....ee.hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh...eeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocg A   1 MKKILIIGGVAGGASAAARARRLSETAEIIMFERGEYVSFANCGLPYHISGEIAQRSALVLQTPESFKARFNVEVRVKHEVVAIDRAAKLVTVRRLLDGSEYQESYDTLLLSPGAAPIVPPIPGVDNPLTHSLRNIPDMDRILQTIQMNNVEHATVVGGGAIGLEMMESLHHLGIKTTLLELADQVMTPVDREMAGFAHQAIRDQGVDLRLGTALSEVSYQVQTHVASDAAGEDTAHQHIKGHLSLTLSNGELLETDLLIMAIGVRPETQLARDAGLAIGELGGIKVNAMMQTSDPAIYAVGDAVEEQDFVTGQACLVPLAGPANRQGRMAADNMFGREERYQGTQGTAICKVFDLAVGATGKNEKQLKQAGIAFEKVYVHTASHASYYPGAEVVSFKLLFDPVKGTIFGAQAVGKDGIDKRIDVMAVAQRAGMTVEQLQHLELSYAPPYGSAKDVINQAAFVASNIIKGDATPIHFDQIDNLSEDQLLLDVRNPGELQNGGLEGAVNIPVDELRDRMHELPKDKEIIIFCQVGLRGNVAYRQLVNNGYRARNLIGGYRTYKFAS 565
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560     


Chain B from PDB  Type:PROTEIN  Length:565
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhh...eeeeee.......hhhhhhhhhh....hhhhhh..hhhhhhhhhh.eeee.eeeeeee....eeeeee.....eeeee..eeee...eee............eee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh..eee....eeeeeee.....................eeeeee....eeee..eee...eee.hhhhhhh.........ee...........eee....eeee......ee...hhhhhhhhhhhhhhhhh............eeeee..eeeeeee.hhhhhhh.....eeeeeeee..........eeeeeeee......eeeeeeee..hhhhhhhhhhhhhhh..hhhhhh..............hhhhhhhhhhhhhhh....ee...........eeeee..hhhhhhhh.....ee.hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh..eeeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocg B   1 MKKILIIGGVAGGASAAARARRLSETAEIIMFERGEYVSFANCGLPYHISGEIAQRSALVLQTPESFKARFNVEVRVKHEVVAIDRAAKLVTVRRLLDGSEYQESYDTLLLSPGAAPIVPPIPGVDNPLTHSLRNIPDMDRILQTIQMNNVEHATVVGGGAIGLEMMESLHHLGIKTTLLELADQVMTPVDREMAGFAHQAIRDQGVDLRLGTALSEVSYQVQTHVASDAAGEDTAHQHIKGHLSLTLSNGELLETDLLIMAIGVRPETQLARDAGLAIGELGGIKVNAMMQTSDPAIYAVGDAVEEQDFVTGQACLVPLAGPANRQGRMAADNMFGREERYQGTQGTAICKVFDLAVGATGKNEKQLKQAGIAFEKVYVHTASHASYYPGAEVVSFKLLFDPVKGTIFGAQAVGKDGIDKRIDVMAVAQRAGMTVEQLQHLELSYAPPYGSAKDVINQAAFVASNIIKGDATPIHFDQIDNLSEDQLLLDVRNPGELQNGGLEGAVNIPVDELRDRMHELPKDKEIIIFCQVGLRGNVAYRQLVNNGYRARNLIGGYRTYKFAS 565
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560
   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 4OCG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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