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(-) Description

Title :  CRYSTAL STRUCTURE OF SULFIDE:QUINONE OXIDOREDUCTASE FROM ACIDITHIOBACILLUS FERROOXIDANS, C160A MUTANT
 
Authors :  M. M. Cherney, Y. Zhang, M. Solomonson, J. H. Weiner, M. N. G. James
Date :  16 Nov 09  (Deposition) - 07 Apr 10  (Release) - 28 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductases, Sulfide:Quinone Oxidoreductase, C160A Mutant, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Cherney, Y. Zhang, M. Solomonson, J. H. Weiner, M. N. James
Crystal Structure Of Sulfide:Quinone Oxidoreductase From Acidithiobacillus Ferrooxidans: Insights Into Sulfidotrophic Respiration And Detoxification.
J. Mol. Biol. V. 398 292 2010
PubMed-ID: 20303979  |  Reference-DOI: 10.1016/J.JMB.2010.03.018

(-) Compounds

Molecule 1 - SULFIDE-QUINONE REDUCTASE, PUTATIVE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLM1
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AFE_1792
    Mutation: YES
    Organism Common: FERROBACILLUS FERROOXIDANS (STRAIN ATCC 23270)
    Organism Scientific: ACIDITHIOBACILLUS FERROOXIDANS ATCC 23270
    Organism Taxid: 243159
    Strain: ATCC 23270 / DSM 14882 / NCIB 8455

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2H2S2Ligand/IonHYDROSULFURIC ACID
3LMT1Ligand/IonDODECYL-BETA-D-MALTOSIDE
4PGR1Ligand/IonR-1,2-PROPANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:7 , GLY A:8 , ALA A:9 , GLY A:10 , THR A:11 , GLY A:12 , SER A:34 , ALA A:35 , VAL A:42 , PRO A:43 , SER A:77 , ALA A:78 , ALA A:104 , THR A:105 , GLY A:106 , PRO A:107 , ILE A:127 , PRO A:163 , VAL A:267 , GLY A:301 , ILE A:302 , LYS A:320 , THR A:321 , GLY A:322 , VAL A:355 , PHE A:357 , LYS A:391 , HOH A:435 , HOH A:437 , HOH A:443 , HOH A:455 , HOH A:457 , HOH A:471 , HOH A:474 , H2S A:502 , PGR A:504 , HOH A:649 , HOH A:653 , HOH A:701 , HOH A:734 , HOH A:737BINDING SITE FOR RESIDUE FAD A 500
2AC2SOFTWARETYR A:165 , GLY A:205 , ASP A:206 , ILE A:210 , GLU A:217 , ALA A:358 , ALA A:365 , PHE A:367 , TYR A:383 , HOH A:448 , HOH A:470 , HOH A:479 , HOH A:490 , HOH A:713BINDING SITE FOR RESIDUE LMT A 501
3AC3SOFTWARECYS A:356 , HOH A:489 , FAD A:500 , HOH A:656BINDING SITE FOR RESIDUE H2S A 502
4AC4SOFTWARESER A:159 , PHE A:264 , LYS A:320 , HOH A:507BINDING SITE FOR RESIDUE H2S A 503
5AC5SOFTWARECYS A:356 , PHE A:357 , LYS A:391 , PHE A:394 , FAD A:500BINDING SITE FOR RESIDUE PGR A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:370 -Pro A:371
2Lys A:374 -Pro A:375

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KPK)

(-) 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:418
 aligned with SQRD_ACIF2 | B7JBP8 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:418
                                    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        
           SQRD_ACIF2     1 MAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSICTVDHAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVSEPFYEKVLFKM 418
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhh...eeeee....eee...hhhhhhh...hhhhheeehhhhhhh...eee...eeeee....eeee....eee..eeee...eee.hhhh.........ee...hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..............hhhhhhhhhhhhh..eee..eeeeeee..eeeeeee.....eeeeeeee..eeeee..eeehhhhhh........................eee.....................hhhhhhhhhhhhhhhhhhhh.............eeeeee....eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kpk A   1 MAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSICTVDHAERAFAEYQALLREPGPIVIGAMAGASAFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVSEPFYEKVLFKM 418
                                    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
   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 3KPK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KPK)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SQRD_ACIF2 | B7JBP8)
molecular function
    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.
    GO:0048038    quinone binding    Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
biological process
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  Cis Peptide Bonds
    Leu A:370 - Pro A:371   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        SQRD_ACIF2 | B7JBP8: 3sx6 3sxi 3sy4 3syi 3sz0 3szc 3szf 3szw 3t0k 3t14 3t2k 3t2y 3t2z 3t31

(-) Related Entries Specified in the PDB File

3kpg 3kpi