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(-) Description

Title :  CRYSTAL STRUCTURE OF SULFIDE:QUINONE OXIDOREDUCTASE CYS128SER VARIANT FROM ACIDITHIOBACILLUS FERROOXIDANS IN COMPLEX WITH DECYLUBIQUINONE
 
Authors :  M. M. Cherney, Y. Zhang, M. N. G. James, J. H. Weiner
Date :  19 Jul 11  (Deposition) - 16 May 12  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Sulfide:Quinone Oxidoreductase, Cys128Ser Variant, Integral Monotopic Membrane Protein, Complex With Decylubiquinone, 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 Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1DCQ1Ligand/Ion2-DECYL-5,6-DIMETHOXY-3-METHYLCYCLOHEXA-2,5-DIENE-1,4-DIONE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3H2S4Ligand/IonHYDROSULFURIC ACID
4LMT1Ligand/IonDODECYL-BETA-D-MALTOSIDE
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 16)
No.NameCountTypeFull Name
1DCQ2Ligand/Ion2-DECYL-5,6-DIMETHOXY-3-METHYLCYCLOHEXA-2,5-DIENE-1,4-DIONE
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3H2S8Ligand/IonHYDROSULFURIC ACID
4LMT2Ligand/IonDODECYL-BETA-D-MALTOSIDE
5SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
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 , SER A:128 , PRO A:163 , VAL A:267 , GLY A:301 , ILE A:302 , THR A:321 , GLY A:322 , ILE A:325 , VAL A:355 , CYS A:356 , PHE A:357 , LYS A:391 , DCQ A:502 , H2S A:506 , HOH A:601 , HOH A:602 , HOH A:609 , HOH A:610 , HOH A:654 , HOH A:660 , HOH A:702 , HOH A:716 , HOH A:718 , HOH A:740 , HOH A:776BINDING SITE FOR RESIDUE FAD A 500
2AC2SOFTWAREGLY A:205 , ASP A:206 , ILE A:210 , GLU A:217 , CYS A:356 , ALA A:358 , ALA A:365 , TYR A:383 , HOH A:622 , HOH A:650 , HOH A:710 , HOH A:719 , HOH A:738 , HOH A:742 , HOH A:753 , HOH A:779BINDING SITE FOR RESIDUE LMT A 501
3AC3SOFTWAREPHE A:41 , PRO A:43 , GLY A:322 , TYR A:323 , VAL A:355 , PHE A:357 , LYS A:391 , PHE A:394 , TYR A:411 , LYS A:417 , FAD A:500 , HOH A:860BINDING SITE FOR RESIDUE DCQ A 502
4AC4SOFTWAREMET A:-2 , HIS A:3 , HIS A:97 , HOH A:687BINDING SITE FOR RESIDUE SO4 A 503
5AC5SOFTWARESER A:126 , ILE A:127 , SER A:128 , ILE A:261 , PRO A:262BINDING SITE FOR RESIDUE H2S A 504
6AC6SOFTWAREPHE A:161 , GLY A:162 , CYS A:356 , H2S A:506 , HOH A:887BINDING SITE FOR RESIDUE H2S A 505
7AC7SOFTWARETHR A:321 , VAL A:355 , CYS A:356 , FAD A:500 , H2S A:505BINDING SITE FOR RESIDUE H2S A 506
8AC8SOFTWARECYS A:160BINDING SITE FOR RESIDUE H2S A 507

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:370 -Pro A:371
2Lys A:374 -Pro A:375
3Ser A:407 -Glu A:408

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SZW)

(-) Sequences/Alignments

Asymmetric 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:421
 aligned with SQRD_ACIF2 | B7JBP8 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:421
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417 
           SQRD_ACIF2     - ---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......hhhhhhhhhhhhhhhhhh.hhhhh..eeeee..............hhhhhhhhhhhhh..eee..eeeeeee..eeeeeee.....eeeeeeee..eeeee..eeehhhhhh........................eee.hhhh................hhhhhhhhhhhhhhhhhhhhh............eeeeee....eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3szw A  -2 MRGSAHVVILGAGTGGMPAAYEMKEALGSGHEVTLISANDYFQFVPSNPWVGVGWKERDDIAFPIRHYVERKGIHFIAQSAEQIDAEAQNITLADGNTVHYDYLMIATGPKLAFENVPGSDPHEGPVQSISTVDHAERAFAEYQALLREPGPIVIGAMAGASCFGPAYEYAMIVASDLKKRGMRDKIPSFTFITSEPYIGHLGIQGVGDSKGILTKGLKEEGIEAYTNCKVTKVEDNKMYVTQVDEKGETIKEMVLPVKFGMMIPAFKGVPAVAGVEGLCNPGGFVLVDEHQRSKKYANIFAAGIAIAIPPVETTPVPTGAPKTGYMIESMVSAAVHNIKADLEGRKGEQTMGTWNAVCFADMGDRGAAFIALPQLKPRKVDVFAYGRWVHLAKVAFEKYFIRKMKMGVSEPFYEKVLFKM 418
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417
   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 3SZW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric 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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 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 3t0k 3t14 3t2k 3t2y 3t2z 3t31

(-) Related Entries Specified in the PDB File

3hyv 3hyw 3hyx 3kpg 3kpi 3kpk 3sx6 3sxi 3sy4 3syi 3sz0 3szc 3szf 3t0k 3t14 3t2k 3t2y 3t2z 3t31