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(-) Description

Title :  STRUCTURE OF THE SHEWANELLA LOIHICA PV-4 NADH-DEPENDENT PERSULFIDE REDUCTASE C531S MUTANT
 
Authors :  M. H. Sazinsky, M. D. Warner, V. Lukose, K. H. Lee, E. J. Crane
Date :  03 Jul 10  (Deposition) - 08 Dec 10  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fad, Coa, Persulfide Reductase, Rhodanese, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Warner, V. Lukose, K. H. Lee, K. Lopez, M. H Sazinsky, E. J. Crane
Characterization Of An Nadh-Dependent Persulfide Reductase From Shewanella Loihica Pv-4: Implications For The Mechanis Of Sulfur Respiration Via Fad-Dependent Enzymes .
Biochemistry V. 50 194 2010
PubMed-ID: 21090815  |  Reference-DOI: 10.1021/BI101232Y

(-) Compounds

Molecule 1 - FAD-DEPENDENT PYRIDINE NUCLEOTIDE-DISULPHIDE OXIDOREDUCTASE
    Chains: A, B
    EC Number: 1.8.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET21B+
    Gene: SHEW_0729
    Mutation: YES
    Organism Scientific: SHEWANELLA LOIHICA
    Organism Taxid: 323850
    Strain: ATCC BAA-1088 / PV-4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2COA2Ligand/IonCOENZYME A
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:11 , ALA A:14 , ARG A:19 , ARG A:22 , SER A:39 , PHE A:40 , ASN A:42 , CYS A:43 , ALA A:321 , ASN A:325 , ARG A:329 , HOH A:636 , HOH A:638 , HOH A:655 , HOH A:659 , HOH A:711 , HOH A:792 , FAD A:900 , HOH A:948 , 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:538 , HOH B:708BINDING SITE FOR RESIDUE COA A 901
2AC2SOFTWAREALA A:231 , SER A:531 , GLN A:532 , VAL A:533 , LEU A:535 , ARG A:536BINDING SITE FOR RESIDUE CL A 566
3AC3SOFTWAREGLY A:8 , VAL A:10 , ALA A:11 , GLY A:12 , 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 , PHE A:161 , ILE A:162 , GLY A:302 , ASP A:303 , PRO A:319 , LEU A:320 , ALA A:321 , HOH A:597 , HOH A:606 , HOH A:631 , HOH A:665 , HOH A:669 , HOH A:695 , HOH A:719 , HOH A:857 , COA A:901 , TYR B:446 , ALA B:447 , PRO B:448BINDING SITE FOR RESIDUE FAD A 900
4AC4SOFTWAREALA B:231 , SER B:531 , GLN B:532 , VAL B:533 , LEU B:535 , ARG B:536BINDING SITE FOR RESIDUE CL B 566
5AC5SOFTWARETYR 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 , PHE B:161 , ILE B:162 , LEU B:271 , GLY B:302 , ASP B:303 , PRO B:319 , LEU B:320 , ALA B:321 , HOH B:574 , HOH B:575 , HOH B:585 , HOH B:598 , HOH B:610 , HOH B:639 , HOH B:657 , HOH B:683 , HOH B:763BINDING SITE FOR RESIDUE FAD B 900
6AC6SOFTWARETYR 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:613 , HOH A:637 , HOH A:663 , 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 , GLN B:62 , ALA B:321 , ASN B:325 , ARG B:329 , HOH B:650 , HOH B:651 , HOH B:653 , HOH B:840 , HOH B:876 , HOH B:961 , HOH B:1091BINDING SITE FOR RESIDUE COA B 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NTD)

(-) 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:565
 aligned with A3QAV3_SHELP | A3QAV3 from UniProtKB/TrEMBL  Length:566

    Alignment length: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     
         A3QAV3_SHELP     1 MKKILIIGGVAGGASAAARARRLSETAEIIMFERGEYVSFANCGLPYHISGEIAQRSALVLQTPESFKARFNVEVRVKHEVVAIDRAAKLVTVRRLLDGSEYQESYDTLLLSPGAAPIVPPIPGVDNPLTHSLRNIPDMDRILQTIQMNNVEHATVVGGGFIGLEMMESLHHLGIKTTLLELADQVMTPVDREMAGFAHQAIRDQGVDLRLGTALSEVSYQVQTHVASDAAGEDTAHQHIKGHLSLTLSNGELLETDLLIMAIGVRPETQLARDAGLAIGELGGIKVNAMMQTSDPAIYAVGDAVEEQDFVTGQACLVPLAGPANRQGRMAADNMFGREERYQGTQGTAICKVFDLAVGATGKNEKQLKQAGIAFEKVYVHTASHASYYPGAEVVSFKLLFDPVKGTIFGAQAVGKDGIDKRIDVMAVAQRAGMTVEQLQHLELSYAPPYGSAKDVINQAAFVASNIIKGDATPIHFDQIDNLSEDQLLLDVRNPGELQNGGLEGAVNIPVDELRDRMHELPKDKEIIIFCQVGLRGNVAYRQLVNNGYRARNLIGGYRTYKFAS 565
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhh....hhhhhh..hhhhhhhhhh.eee..eeeeeee....eeeeee.....eeeee..eeee...eee............ee...hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhh..eeee...eeeeeee......hhhhh..........eeeeee....eeee.eeee...eee.hhhhhhhh.....................eee.hhhh.ee......ee...hhhhhhhhhhhhhhhhh............eeeee..eeeeeee.hhhhhhhh....eeeeeeee..........eeeeeeee......eeeeeeee..hhhhhhhhhhhhhhh..hhhhhh..............hhhhhhhhhhhhhhh....ee...........eeeee..hhhhhhhh.....ee.hhhhh..hhhhh....eeeee...hhhhhhhhhhhhhh...eeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ntd A   1 MKKILIIGGVAGGASAAARARRLSETAEIIMFERGEYVSFANCGLPYHISGEIAQRSALVLQTPESFKARFNVEVRVKHEVVAIDRAAKLVTVRRLLDGSEYQESYDTLLLSPGAAPIVPPIPGVDNPLTHSLRNIPDMDRILQTIQMNNVEHATVVGGGFIGLEMMESLHHLGIKTTLLELADQVMTPVDREMAGFAHQAIRDQGVDLRLGTALSEVSYQVQTHVASDAAGEDTAHQHIKGHLSLTLSNGELLETDLLIMAIGVRPETQLARDAGLAIGELGGIKVNAMMQTSDPAIYAVGDAVEEQDFVTGQACLVPLAGPANRQGRMAADNMFGREERYQGTQGTAICKVFDLAVGATGKNEKQLKQAGIAFEKVYVHTASHASYYPGAEVVSFKLLFDPVKGTIFGAQAVGKDGIDKRIDVMAVAQRAGMTVEQLQHLELSYAPPYGSAKDVINQAAFVASNIIKGDATPIHFDQIDNLSEDQLLLDVRNPGELQNGGLEGAVNIPVDELRDRMHELPKDKEIIIFSQVGLRGNVAYRQLVNNGYRARNLIGGYRTYKFAS 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
 aligned with A3QAV3_SHELP | A3QAV3 from UniProtKB/TrEMBL  Length:566

    Alignment length: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     
         A3QAV3_SHELP     1 MKKILIIGGVAGGASAAARARRLSETAEIIMFERGEYVSFANCGLPYHISGEIAQRSALVLQTPESFKARFNVEVRVKHEVVAIDRAAKLVTVRRLLDGSEYQESYDTLLLSPGAAPIVPPIPGVDNPLTHSLRNIPDMDRILQTIQMNNVEHATVVGGGFIGLEMMESLHHLGIKTTLLELADQVMTPVDREMAGFAHQAIRDQGVDLRLGTALSEVSYQVQTHVASDAAGEDTAHQHIKGHLSLTLSNGELLETDLLIMAIGVRPETQLARDAGLAIGELGGIKVNAMMQTSDPAIYAVGDAVEEQDFVTGQACLVPLAGPANRQGRMAADNMFGREERYQGTQGTAICKVFDLAVGATGKNEKQLKQAGIAFEKVYVHTASHASYYPGAEVVSFKLLFDPVKGTIFGAQAVGKDGIDKRIDVMAVAQRAGMTVEQLQHLELSYAPPYGSAKDVINQAAFVASNIIKGDATPIHFDQIDNLSEDQLLLDVRNPGELQNGGLEGAVNIPVDELRDRMHELPKDKEIIIFCQVGLRGNVAYRQLVNNGYRARNLIGGYRTYKFAS 565
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-3ntdB01 B:153-231                                                    --------------------------------------------------------------------------------------------------------------------Pyr_redox_dim-3ntdB05 B:348-457                                                                               --------------------Rhodanese-3ntdB07 B:478-564                                                            - Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-3ntdB02 B:153-231                                                    --------------------------------------------------------------------------------------------------------------------Pyr_redox_dim-3ntdB06 B:348-457                                                                               --------------------Rhodanese-3ntdB08 B:478-564                                                            - Pfam domains (2)
           Pfam domains (3) --Pyr_redox_2-3ntdB03 B:3-309                                                                                                                                                                                                                                                                                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --Pyr_redox_2-3ntdB04 B:3-309                                                                                                                                                                                                                                                                                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeeee....hhhhhhhhhhhhh...eeeee........hhhhhhhhhh....hhhhhh..hhhhhhhhhh.eee..eeeeeee....eeeeee.....eeeee..eeee...eee............ee...hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh..eee....eeeeeee.....................eeeeee....eeee.eeee...eee.hhhhhhhh.....................eee.hhhh.ee......ee...hhhhhhhhhhhhhhhhh............eeeee..eeeeeee.hhhhhhhh....eeeeeeee..........eeeeeeee......eeeeeeee..hhhhhhhhhhhhhhh..hhhhhh..............hhhhhhhhhhhhhhh....ee...........eeeee..hhhhhh.......ee.hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh....eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ntd B   1 MKKILIIGGVAGGASAAARARRLSETAEIIMFERGEYVSFANCGLPYHISGEIAQRSALVLQTPESFKARFNVEVRVKHEVVAIDRAAKLVTVRRLLDGSEYQESYDTLLLSPGAAPIVPPIPGVDNPLTHSLRNIPDMDRILQTIQMNNVEHATVVGGGFIGLEMMESLHHLGIKTTLLELADQVMTPVDREMAGFAHQAIRDQGVDLRLGTALSEVSYQVQTHVASDAAGEDTAHQHIKGHLSLTLSNGELLETDLLIMAIGVRPETQLARDAGLAIGELGGIKVNAMMQTSDPAIYAVGDAVEEQDFVTGQACLVPLAGPANRQGRMAADNMFGREERYQGTQGTAICKVFDLAVGATGKNEKQLKQAGIAFEKVYVHTASHASYYPGAEVVSFKLLFDPVKGTIFGAQAVGKDGIDKRIDVMAVAQRAGMTVEQLQHLELSYAPPYGSAKDVINQAAFVASNIIKGDATPIHFDQIDNLSEDQLLLDVRNPGELQNGGLEGAVNIPVDELRDRMHELPKDKEIIIFSQVGLRGNVAYRQLVNNGYRARNLIGGYRTYKFAS 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)
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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 3NTD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (4, 8)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Pyr_redox_dim] (44)
(-)
Clan: no clan defined [family: Rhodanese] (33)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A3QAV3_SHELP | A3QAV3)
molecular function
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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 Related Entries

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        A3QAV3_SHELP | A3QAV3: 3nt6 3nta 4ocg

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3nt6 3nta