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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE ARG409LEU VARIANTS OF KATG FROM HALOARCULA MARISMORTUI
 
Authors :  T. Sato, W. Higuchi, K. Yoshimatsu, T. Fujiwara
Date :  01 Dec 11  (Deposition) - 05 Dec 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Catalase-Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Sato, W. Higuchi, K. Yoshimatsu, T. Fujiwara
Catalatic Implication Guided By Structure, Kinetics And Theoretical Studies On Ser305Thr And Arg409Leu Variants Of Hmkatg
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CATALASE-PEROXIDASE 2
    Chains: A, B
    EC Number: 1.11.1.21
    Engineered: YES
    Expression System: HALOFERAX VOLCANII
    Expression System Taxid: 2246
    Gene: KATG2
    Mutation: YES
    Organism Scientific: HALOARCULA MARISMORTUI
    Organism Taxid: 272569
    Strain: ATCC 43049
    Synonym: KATG, CP 2, PEROXIDASE/CATALASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:88 , LEU A:89 , TRP A:95 , TYR A:218 , PRO A:221 , PHE A:241 , LEU A:254 , GLY A:258 , HIS A:259 , PHE A:261 , GLY A:262 , LYS A:263 , VAL A:264 , HIS A:265 , THR A:304 , SER A:305 , TRP A:311 , THR A:371 , TRP A:403BINDING SITE FOR RESIDUE HEM A 800
2AC2SOFTWAREPRO B:88 , TRP B:95 , PRO B:221 , PHE B:241 , LEU B:254 , ILE B:255 , GLY B:258 , HIS B:259 , PHE B:261 , GLY B:262 , LYS B:263 , VAL B:264 , HIS B:265 , THR B:304 , SER B:305 , TRP B:311 , THR B:371 , PHE B:399 , TRP B:403 , HOH B:757 , HOH B:829 , HOH B:844BINDING SITE FOR RESIDUE HEM B 800

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:118 -Pro A:119
2Glu A:491 -Pro A:492
3Ala B:118 -Pro B:119
4Glu B:491 -Pro B:492

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.KATG2_HALMA87-98
 		  2A:87-98
B:87-98
2PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.KATG2_HALMA251-261
 		  2A:251-261
B:251-261

(-) Exons   (0, 0)

(no "Exon" information available for 3VLH)

(-) 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:710
 aligned with KATG2_HALMA | O59651 from UniProtKB/Swiss-Prot  Length:731

    Alignment length:714
                                    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       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727    
          KATG2_HALMA    18 KRPKSNQDWWPSKLNLEILDQNARDVGPVEDDFDYAEEFQKLDLEAVKSDLEELMTSSQDWWPADYGHYGPLFIRMAWHSAGTYRTADGRGGAAGGRQRFAPINSWPDNANLDKARRLLLPIKQKYGQKISWADLMILAGNVAIESMGFKTFGYAGGREDAFEEDKAVNWGPEDEFETQERFDEPGEIQEGLGASVMGLIYVNPEGPDGNPDPEASAKNIRQTFDRMAMNDKETAALIAGGHTFGKVHGADDPEENLGPEPEAAPIEQQGLGWQNKNGNSKGGEMITSGIEGPWTQSPTEWDMGYINNLLDYEWEPEKGPGGAWQWAPKSEELKNSVPDAHDPDEKQTPMMLTTDIALKRDPDYREVMETFQENPMEFGMNFAKAWYKLTHRDMGPPERFLGPEVPDEEMIWQDPLPDADYDLIGDEEIAELKEEILDSDLSVSQLVKTAWASASTYRDSDKRGGANGARLRLEPQKNWEVNEPEQLETVLGTLENIQTEFNDSRSDGTQVSLADLIVLGGNAAVEQAAANAGYDVEIPFEPGRVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDNADLLNLTASELTALIGGMRSIGANYQDTDLGVFTDEPETLTNDFFVNLLDMGTEWEPAADSEHRYKGLDRDTGEVKWEATRIDLIFGSNDRLRAISEVYGSADAEKKLVHDFVDTWSKVMKLDRFDLE 731
               SCOP domains d3vlha1 A:18-423 automated matches                                                                                                                                                                                                                                                                                                                                                                                    d3vlha2 A:424-731 automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh.....hhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................................................hhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...ee....hhhhhh..hhhhhhhhhh........----..........ee.........hhhhhhhhhh.eeeee.....eeeee........ee.......ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhh..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh..ee....ee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh.............hhhhhhhhh..eeeee......eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------------------------------------------------PEROXIDASE_-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vlh A  18 KRPKSNQDWWPSKLNLEILDQNARDVGPVEDDFDYAEEFQKLDLEAVKSDLEELMTSSQDWWPADYGHYGPLFIRMAWHSAGTYRTADGRGGAAGGRQRFAPINSWPDNANLDKARRLLLPIKQKYGQKISWADLMILAGNVAIESMGFKTFGYAGGREDAFEEDKAVNWGPEDEFETQERFDEPGEIQEGLGASVMGLIYVNPEGPDGNPDPEASAKNIRQTFDRMAMNDKETAALIAGGHTFGKVHGADDPEENLGPEPEAAPIEQQGLGWQNKN----GGEMITSGIEGPWTQSPTEWDMGYINNLLDYEWEPEKGPGGAWQWAPKSEELKNSVPDAHDPDEKQTPMMLTTDIALKRDPDYREVMETFQENPMEFGMNFAKAWYKLTHLDMGPPERFLGPEVPDEEMIWQDPLPDADYDLIGDEEIAELKEEILDSDLSVSQLVKTAWASASTYRDSDKRGGANGARLRLEPQKNWEVNEPEQLETVLGTLENIQTEFNDSRSDGTQVSLADLIVLGGNAAVEQAAANAGYDVEIPFEPGRVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDNADLLNLTASELTALIGGMRSIGANYQDTDLGVFTDEPETLTNDFFVNLLDMGTEWEPAADSEHRYKGLDRDTGEVKWEATRIDLIFGSNDRLRAISEVYGSADAEKKLVHDFVDTWSKVMKLDRFDLE 731
                                    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      |  - |     307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727    
                                                                                                                                                                                                                                                                                                              294  299                                                                                                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:714
 aligned with KATG2_HALMA | O59651 from UniProtKB/Swiss-Prot  Length:731

    Alignment length:714
                                    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       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727    
          KATG2_HALMA    18 KRPKSNQDWWPSKLNLEILDQNARDVGPVEDDFDYAEEFQKLDLEAVKSDLEELMTSSQDWWPADYGHYGPLFIRMAWHSAGTYRTADGRGGAAGGRQRFAPINSWPDNANLDKARRLLLPIKQKYGQKISWADLMILAGNVAIESMGFKTFGYAGGREDAFEEDKAVNWGPEDEFETQERFDEPGEIQEGLGASVMGLIYVNPEGPDGNPDPEASAKNIRQTFDRMAMNDKETAALIAGGHTFGKVHGADDPEENLGPEPEAAPIEQQGLGWQNKNGNSKGGEMITSGIEGPWTQSPTEWDMGYINNLLDYEWEPEKGPGGAWQWAPKSEELKNSVPDAHDPDEKQTPMMLTTDIALKRDPDYREVMETFQENPMEFGMNFAKAWYKLTHRDMGPPERFLGPEVPDEEMIWQDPLPDADYDLIGDEEIAELKEEILDSDLSVSQLVKTAWASASTYRDSDKRGGANGARLRLEPQKNWEVNEPEQLETVLGTLENIQTEFNDSRSDGTQVSLADLIVLGGNAAVEQAAANAGYDVEIPFEPGRVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDNADLLNLTASELTALIGGMRSIGANYQDTDLGVFTDEPETLTNDFFVNLLDMGTEWEPAADSEHRYKGLDRDTGEVKWEATRIDLIFGSNDRLRAISEVYGSADAEKKLVHDFVDTWSKVMKLDRFDLE 731
               SCOP domains d3vlhb1 B:18-423 automated matches                                                                                                                                                                                                                                                                                                                                                                                    d3vlhb2 B:424-731 automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh.....hhhhhh............hhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................................................hhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...ee....hhhhhh..hhhhhhhhhh...........hhhhh......ee.........hhhhhhhhhh.eeeee.....eeeee........ee.......ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhh..........hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh..ee....ee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh.............hhhhhhhh...eeeee.......eeeee.....eeeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------------------------------------------------PEROXIDASE_-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vlh B  18 KRPKSNQDWWPSKLNLEILDQNARDVGPVEDDFDYAEEFQKLDLEAVKSDLEELMTSSQDWWPADYGHYGPLFIRMAWHSAGTYRTADGRGGAAGGRQRFAPINSWPDNANLDKARRLLLPIKQKYGQKISWADLMILAGNVAIESMGFKTFGYAGGREDAFEEDKAVNWGPEDEFETQERFDEPGEIQEGLGASVMGLIYVNPEGPDGNPDPEASAKNIRQTFDRMAMNDKETAALIAGGHTFGKVHGADDPEENLGPEPEAAPIEQQGLGWQNKNGNSKGGEMITSGIEGPWTQSPTEWDMGYINNLLDYEWEPEKGPGGAWQWAPKSEELKNSVPDAHDPDEKQTPMMLTTDIALKRDPDYREVMETFQENPMEFGMNFAKAWYKLTHLDMGPPERFLGPEVPDEEMIWQDPLPDADYDLIGDEEIAELKEEILDSDLSVSQLVKTAWASASTYRDSDKRGGANGARLRLEPQKNWEVNEPEQLETVLGTLENIQTEFNDSRSDGTQVSLADLIVLGGNAAVEQAAANAGYDVEIPFEPGRVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDNADLLNLTASELTALIGGMRSIGANYQDTDLGVFTDEPETLTNDFFVNLLDMGTEWEPAADSEHRYKGLDRDTGEVKWEATRIDLIFGSNDRLRAISEVYGSADAEKKLVHDFVDTWSKVMKLDRFDLE 731
                                    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       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KATG2_HALMA | O59651)
molecular function
    GO:0004096    catalase activity    Catalysis of the reaction: 2 hydrogen peroxide = O2 + 2 H2O.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    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:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

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  3vlh
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  1.11.1.21
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 Related Entries

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

UniProtKB/Swiss-Prot
        KATG2_HALMA | O59651: 1itk 3uw8 3vli 3vlj 3vlk 3vll 3vlm

(-) Related Entries Specified in the PDB File

3uw8 SER305THR VARIANT
3vli CYANIDE ARG409LEU VARIANT
3vlj CYANIDE ARG409LEU VARIANT COMPLEXES WITH O-DIANISIDINE
3vlk SER305ALA VARIANT
3vll SER305ALA VARIANT COMPLEXES WITH INHIBITOR SHA
3vlm MET244ALA VARIANT