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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ELECTRON TRANSFER COMPLEX RUBREDOXIN - RUBREDOXIN REDUCTASE FROM PSEUDOMONAS AERUGINOSA.
 
Authors :  G. Hagelueken, L. Wiehlmann, T. M. Adams, H. Kolmar, D. W. Heinz, B. Tuem W. -D. Schubert
Date :  14 Jun 07  (Deposition) - 14 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alkane Degradation, Iron-Sulfur Protein, Oxidoreductase, Electron Transfer, Electron Transport, Fad, Nad, Iron, Flavoprotein, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Hagelueken, L. Wiehlmann, T. M. Adams, H. Kolmar, D. W. Heinz, B. Tuemmler, W. -D. Schubert
Crystal Structure Of The Electron Transfer Complex Rubredoxin - Rubredoxin Reductase From Pseudomonas Aeruginosa.
Proc. Natl. Acad. Sci. Usa V. 104 12276 2007
PubMed-ID: 17636129  |  Reference-DOI: 10.1073/PNAS.0702919104

(-) Compounds

Molecule 1 - RUBREDOXIN REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
 
Molecule 2 - RUBREDOXIN 2
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: RUBREDOXIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FE1Ligand/IonFE (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:10 , GLY A:11 , THR A:12 , GLY A:13 , LEU A:14 , ALA A:15 , THR A:36 , ALA A:37 , ASP A:38 , LYS A:45 , PRO A:46 , THR A:81 , ARG A:82 , VAL A:83 , ALA A:108 , TRP A:109 , GLY A:110 , ILE A:156 , GLU A:159 , PHE A:160 , GLY A:276 , ASP A:277 , LEU A:287 , TYR A:288 , VAL A:289 , LEU A:292 , LYS A:320 , HOH A:2019 , HOH A:2026 , HOH A:2189 , HOH A:2213 , HOH A:2233 , HOH A:2234 , HOH A:2236 , HOH A:2237 , HOH A:2238 , HOH A:2239 , HOH B:2013BINDING SITE FOR RESIDUE FAD A1385
2AC2SOFTWARECYS B:6 , CYS B:9 , CYS B:39 , CYS B:42BINDING SITE FOR RESIDUE FE B1054

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V3B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V3B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V3B)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RUBREDOXIN_LIKEPS50903 Rubredoxin-like domain profile.RUBR2_PSEAE1-52  1B:1-52
2RUBREDOXINPS00202 Rubredoxin signature.RUBR2_PSEAE33-43  1B:33-43

(-) Exons   (0, 0)

(no "Exon" information available for 2V3B)

(-) 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:381
 aligned with RURE_PSEAE | Q9HTK9 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:381
                                    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 
           RURE_PSEAE     4 RAPLVIIGTGLAGYNLAREWRKLDGETPLLMITADDGRSYSKPMLSTGFSKNKDADGLAMAEPGAMAEQLNARILTHTRVTGIDPGHQRIWIGEEEVRYRDLVLAWGAEPIRVPVEGDAQDALYPINDLEDYARFRQAAAGKRRVLLLGAGLIGCEFANDLSSGGYQLDVVAPCEQVMPGLLHPAAAKAVQAGLEGLGVRFHLGPVLASLKKAGEGLEAHLSDGEVIPCDLVVSAVGLRPRTELAFAAGLAVNRGIVVDRSLRTSHANIYALGDCAEVDGLNLLYVMPLMACARALAQTLAGNPSQVAYGPMPVTVKTPACPLVVSPPPRGMDGQWLVEGSGTDLKVLCRDTAGRVIGYALTGAAVNEKLALNKELPGLMA 384
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhh......eeee........hhhhhhhh.....hhhhhh..hhhhhhhhh..eee......eeehhh.eeee..eeee..eeee...eee............eee..hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhh..eeee...eeeeeee..eeeeee....eeee.eeee...eee.hhhhhhh.......eee..........eee....eee......hhhhhhhhhhhhhhhhh............eee......eeee........eeeeeee..eeeeeee.....eeeeeee.hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3b A   4 RAPLVIIGTGLAGYNLAREWRKLDGETPLLMITADDGRSYSKPMLSTGFSKNKDADGLAMAEPGAMAEQLNARILTHTRVTGIDPGHQRIWIGEEEVRYRDLVLAWGAEPIRVPVEGDAQDALYPINDLEDYARFRQAAAGKRRVLLLGAGLIGCEFANDLSSGGYQLDVVAPCEQVMPGLLHPAAAKAVQAGLEGLGVRFHLGPVLASLKKAGEGLEAHLSDGEVIPCDLVVSAVGLRPRTELAFAAGLAVNRGIVVDRSLRTSHANIYALGDCAEVDGLNLLYVMPLMACARALAQTLAGNPSQVAYGPMPVTVKTPACPLVVSPPPRGMDGQWLVEGSGTDLKVLCRDTAGRVIGYALTGAAVNEKLALNKELPGLMA 384
                                    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 


Chain B from PDB  Type:PROTEIN  Length:53
 aligned with RUBR2_PSEAE | Q9HTK8 from UniProtKB/Swiss-Prot  Length:55

    Alignment length:53
                                    10        20        30        40        50   
          RUBR2_PSEAE     1 MRKWQCVVCGFIYDEALGLPEEGIPAGTRWEDIPADWVCPDCGVGKIDFEMIE  53
               SCOP domains d2v3bb_ B: automated matches                          SCOP domains
               CATH domains 2v3bB00 B:1-53  [code=2.20.28.10, no name defined]    CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eee..............hhhhh...........hhh.eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RUBREDOXIN_LIKE  PDB: B:1-52 UniProt: 1-52          - PROSITE (1)
                PROSITE (2) --------------------------------RUBREDOXIN ---------- PROSITE (2)
                 Transcript ----------------------------------------------------- Transcript
                 2v3b B   1 MRKWQCVVCGFIYDEALGLPEEGIPAGTRWEDIPADWVCPDCGVGKIDFEMIE  53
                                    10        20        30        40        50
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V3B)

(-) Gene Ontology  (10, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RURE_PSEAE | Q9HTK9)
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: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:0015044    rubredoxin-NAD+ reductase activity    Catalysis of the reaction: reduced rubredoxin + NAD+ = oxidized rubredoxin + NADH + H+.
    GO:0015046    rubredoxin-NADP reductase activity    Catalysis of the reaction: reduced rubredoxin + NADP+ = oxidized rubredoxin + NADPH + H+.
biological process
    GO:0043448    alkane catabolic process    The chemical reactions and pathways resulting in the breakdown of an alkane, any acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B   (RUBR2_PSEAE | Q9HTK8)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0043448    alkane catabolic process    The chemical reactions and pathways resulting in the breakdown of an alkane, any acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(-) Related Entries Specified in the PDB File

2v3a CRYSTAL STRUCTURE OF RUBREDOXIN REDUCTASE FROM PSEUDOMONAS AERUGINOSA.