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(-) Description

Title :  CRYSTAL STRUCTURE OF SULFIDE:QUINONE OXIDOREDUCTASE HIS132ALA VARIANT FROM ACIDITHIOBACILLUS FERROOXIDANS WITH BOUND DISULFIDE
 
Authors :  M. M. Cherney, Y. Zhang, M. N. G. James, J. H. Weiner
Date :  23 Jul 11  (Deposition) - 16 May 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Sulfide:Quinone Oxidoreductase, His132Ala Variant, Integral Monotopic Membrane Protein, Complex With Disulfide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Cherney, Y. Zhang, M. N. James, J. H. Weiner
Structure-Activity Characterization Of Sulfide:Quinone Oxidoreductase Variants.
J. Struct. Biol. V. 178 319 2012
PubMed-ID: 22542586  |  Reference-DOI: 10.1016/J.JSB.2012.04.007

(-) Compounds

Molecule 1 - SULFIDE-QUINONE REDUCTASE, PUTATIVE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AFE_1792
    Mutation: YES
    Organism Scientific: ACIDITHIOBACILLUS FERROOXIDANS
    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, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2H2S1Ligand/IonHYDROSULFURIC ACID
3LMT1Ligand/IonDODECYL-BETA-D-MALTOSIDE
4S2H1Ligand/IonHYDROGEN DISULFIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
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 , CYS A:160 , PRO A:163 , GLY A:301 , ILE A:302 , LYS A:320 , THR A:321 , GLY A:322 , ILE A:325 , VAL A:355 , PHE A:357 , HOH A:520 , HOH A:522 , HOH A:525BINDING SITE FOR RESIDUE FAD A 500
2AC2SOFTWAREMET A:169 , GLY A:205 , ASP A:206 , ILE A:210 , LEU A:211 , CYS A:356 , ALA A:358 , ALA A:365 , TYR A:383 , HOH A:539 , HOH A:548BINDING SITE FOR RESIDUE LMT A 501
3AC3SOFTWARECYS A:160 , S2H A:505BINDING SITE FOR RESIDUE H2S A 504
4AC4SOFTWAREGLY A:162 , CYS A:356 , H2S A:504BINDING SITE FOR RESIDUE S2H A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T2Y)

(-) 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 3T2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3T2Y)

(-) 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:407
 aligned with SQRD_ACIF2 | B7JBP8 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:407
                                    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       
           SQRD_ACIF2     1 MAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSICTVDHAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVS 407
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhh...eeeeee...eee...hhhhhhh...hhhhheeehhhhhhh...eeee..eeeee....eeee....eee..eeee....ee.hhhh.........ee...hhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..............hhhhhhhhhhhhh..eeee.eeeeeee..eeeeeee.....eeeeeeee..eeeee..ee.hhhhhh........................eee.hhhh................hhhhhhhhhhhhhhhhhhhh.............eeeeee....eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t2y A   1 MAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSICTVDAAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVS 407
                                    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
   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 3T2Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T2Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T2Y)

(-) 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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    Leu A:370 - Pro A:371   [ RasMol ]  
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  3t2y
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3hyv 3hyw 3hyx 3kpg 3kpi 3kpk 3sx6 3sxi 3sy4 3syi 3sz0 3szc 3szf 3szw 3t0k 3t14 3t2k 3t2z 3t31