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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SUCCINATE COMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1
 
Authors :  D. Leys, A. S. Tsapin, T. E. Meyer, M. A. Cusanovich, J. J. Van Beeumen
Date :  03 Oct 99  (Deposition) - 01 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Tetraheme Flavocytochrome C Fumarate Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Leys, A. S. Tsapin, K. H. Nealson, T. E. Meyer, M. A. Cusanovich, J. J. Van Beeumen
Structure And Mechanism Of The Flavocytochrome C Fumarate Reductase Of Shewanella Putrefaciens Mr-1.
Nat. Struct. Biol. V. 6 1113 1999
PubMed-ID: 10581551  |  Reference-DOI: 10.1038/70051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FLAVOCYTOCHROME C FUMARATE REDUCTASE
    Chains: A
    EC Number: 1.3.99.1
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 70863
    Strain: MR-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SIN1Ligand/IonSUCCINIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:62 , HIS A:63 , LEU A:64 , TYR A:83 , CYS A:84 , CYS A:87 , HIS A:88 , PHE A:90 , LEU A:166 , HIS A:337 , VAL A:373 , GLY A:433 , TYR A:434 , LEU A:437BINDING SITE FOR RESIDUE HEM A 601
2AC2SOFTWAREHIS A:42 , GLY A:43 , LEU A:45 , LEU A:48 , PRO A:59 , HIS A:60 , ILE A:68 , ALA A:69 , CYS A:70 , CYS A:73 , HIS A:74 , ASP A:93 , MET A:94 , PRO A:95 , ILE A:202 , TYR A:360 , HEM A:604 , HOH A:720 , HOH A:721 , HOH A:722 , HOH A:748BINDING SITE FOR RESIDUE HEM A 602
3AC3SOFTWAREALA A:6 , GLY A:14 , CYS A:15 , CYS A:18 , HIS A:19 , LYS A:23 , GLY A:24 , GLY A:25 , VAL A:26 , THR A:71 , LYS A:75 , GLY A:76 , HIS A:77 , TYR A:297 , HOH A:745BINDING SITE FOR RESIDUE HEM A 603
4AC4SOFTWARELEU A:5 , PHE A:8 , HIS A:9 , SER A:17 , GLN A:37 , CYS A:38 , CYS A:41 , HIS A:42 , HIS A:74 , PRO A:95 , ARG A:200 , TYR A:325 , ASP A:326 , TYR A:360 , HEM A:602BINDING SITE FOR RESIDUE HEM A 604
5AC5SOFTWAREGLY A:132 , SER A:133 , GLY A:134 , ALA A:136 , LEU A:154 , GLU A:155 , LYS A:156 , GLU A:157 , GLY A:161 , GLY A:162 , ASN A:163 , THR A:164 , ALA A:167 , ALA A:168 , GLY A:169 , GLY A:170 , SER A:275 , ARG A:276 , VAL A:277 , ALA A:312 , GLY A:313 , THR A:335 , ASN A:336 , HIS A:337 , ASP A:343 , MET A:374 , HIS A:503 , HIS A:504 , GLY A:533 , GLU A:534 , ARG A:544 , GLY A:547 , ASN A:548 , ALA A:549 , ILE A:550 , ILE A:553 , SIN A:700 , HOH A:701 , HOH A:702 , HOH A:704 , HOH A:705 , HOH A:717 , HOH A:726BINDING SITE FOR RESIDUE FAD A 600
6AC6SOFTWAREGLY A:169 , MET A:235 , HIS A:364 , THR A:376 , GLU A:377 , ARG A:401 , HIS A:503 , ARG A:544 , GLY A:547 , FAD A:600BINDING SITE FOR RESIDUE SIN A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D4D)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:491 -Pro A:492

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D4D)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.FRDA_SHEON35-118  1A:10-93

(-) Exons   (0, 0)

(no "Exon" information available for 1D4D)

(-) 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:560
 aligned with FRDA_SHEON | P83223 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:566
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588      
           FRDA_SHEON    29 VLADFHGEMGGCDSCHVSDKGGVTNDNLTHENGQCVSCHGDLKELAAAAPKDKVSPHKSHLIGEIACTSCHKGHEKSVAYCDACHSFGFDMPFGGKWERKFVPVDADKAAQDKAIAAGVKETTDVVIIGSGGAGLAAAVSARDAGAKVILLEKEPIPGGNTKLAAGGMNAAETKPQAKLGIEDKKQIMIDDTMKGGRNINDPELVKVLANNSSDSIDWLTSMGADMTDVGRMGGASVNRSHRPTGGAGVGAHVAQVLWDNAVKRGTDIRLNSRVVRILEDASGKVTGVLVKGEYTGYYVIKADAVVIAAGGFAKNNERVSKYDPKLKGFKATNHPGATGDGLDVALQAGAATRDLEYIQAHPTYSPAGGVMITEAVRGNGAIVVNREGNRFMNEITTRDKASAAILQQKGESAYLVFDDSIRKSLKAIEGYVHLNIVKEGKTIEELAKQIDVPAAELAKTVTAYNGFVKSGKDAQFERPDLPRELVVAPFYALEIAPAVHHTMGGLVIDTKAEVKSEKTGKPITGLYAAGEVTGGVHGANRLGGNAISDIVTYGRIAGASAAKFAK 594
               SCOP domains d1d4da1 A:4-102 Flavocytochrome c3 (respiratory fu   marate reductase), N-terminal domain          d1d4da2 A:103-359,A:506-569 Flavocytochrome c3 (respiratory fumarate reductase)                                                                                                                                                                                  d1d4da3 A:360-505 Flavocytochrome c3 (respiratory fumarate reductase)                                                                             d1d4da2 A:103-359,A:506-569                                      SCOP domains
               CATH domains 1d4dA01 A:4-102 Flavocytochrome C3; Chain A                                                        1d4dA02 A:103-360,A:508-568  [code=3.50.50.60, no name defined]                                                                                                                                                                                                   1d4dA03 A:361-505 Flavocytochrome C3; Chain A, domain 1                                                                                          --1d4dA02 A:103-360,A:508-568                                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.....................hhhhhhhhhhhhhhhhhhhhhh.---............hhhhh........hhhhhh......................hhhhhhhhhhh...ee..eeee..hhhhhhhhhhhhh....eeee........hhhhh...ee......hhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eee.........eee.....hhhhhhhhhhhhhhhhh..eee..eeeeeeee.--..eeeeeeee...eeeeee..eeee.......hhhhhhhhhhhhh...........hhhhhhhhhh...ee....eeeeeeee....ee..hhhhhh..eee............hhhhhhhhhhhhhhhheeeeehhhhhh..hhhhhhhhh...eee.hhhhhhhhhh.hhhhhhhhhhhhhhhh-....................eeeeeeeeeeeee..eee.....eee......eeeeeee....ee.........hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------MULTIHEME_CYTC  PDB: A:10-93 UniProt: 35-118                                        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d4d A   4 VLADFHGEMGGCDSCHVSDKGGVTNDNLTHENGQCVSCHGDLKELAAAAP---VSPHKSHLIGEIACTSCHKGHEKSVAYCDACHSFGFDMPFGGKWERKFVPVDADKAAQDKAIAAGVKETTDVVIIGSGGAGLAAAVSARDAGAKVILLEKEPIPGGNTKLAAGGMNAAETKPQAKLGIEDKKQIMIDDTMKGGRNINDPELVKVLANNSSDSIDWLTSMGADMTDVGRMGGASVNRSHRPTGGAGVGAHVAQVLWDNAVKRGTDIRLNSRVVRILED--GKVTGVLVKGEYTGYYVIKADAVVIAAGGFAKNNERVSKYDPKLKGFKATNHPGATGDGLDVALQAGAATRDLQYIQAHPTYSPAGGVMITEAVRGNGAIVVNREGNRFMNEITTRDKASAAILQQKGESAYLVFDDSIRKSLKAIEGYVHLNIVKEGKTIEELAKQIDVPAAELAKTVTAYNGFV-SGKDAQFERPDLPRELVVAPFYALEIAPAVHHTMGGLVIDTKAEVKSEKTAKPITGLYAAGEVTGGVHGANRLGGNAISDIVTYGRIAGASAAKFAK 569
                                    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       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563      
                                                                            53  57                                                                                                                                                                                                                               283  |                                                                                                                                                                                      471 |                                                                                                
                                                                                                                                                                                                                                                                                                                    286                                                                                                                                                                                        473
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D4D)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FRDA_SHEON | P83223)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0000104    succinate dehydrogenase activity    Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
biological process
    GO:0009061    anaerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
    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:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FRDA_SHEON | P83223: 1d4c 1d4e

(-) Related Entries Specified in the PDB File

1d4c UNCOMPLEXED FORM
1d4d SUCCINATE COMPLEXED FORM
1d4e COMPLEXED WITH FUMARATE