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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE MET244ALA VARIANT OF KATG FROM HALOARCULA MARISMORTUI
 
Authors :  T. Sato, T. Ten-I, W. Higuchi, K. Yoshimatsu, T. Fujiwara
Date :  01 Dec 11  (Deposition) - 05 Dec 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Catalase-Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Sato, T. Ten-I, W. Higuchi, K. Yoshimatsu, T. Fujiwara
Crystal Structure And Kinetic Studies On Met244Ala Variant Of Katg From Haloarcula Marismortui
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 , PRO A:221 , ILE A:237 , LEU A:254 , ILE A:255 , GLY A:258 , HIS A:259 , GLY A:262 , LYS A:263 , VAL A:264 , HIS A:265 , THR A:304 , SER A:305 , TRP A:311 , TRP A:403 , HOH A:754BINDING SITE FOR RESIDUE HEM A 800
2AC2SOFTWAREPRO B:88 , TRP B:95 , LEU B:254 , GLY B:258 , HIS B:259 , GLY B:262 , LYS B:263 , VAL B:264 , HIS B:265 , THR B:304 , SER B:305 , THR B:371 , TRP B:403BINDING SITE FOR RESIDUE HEM B 800

(-) SS Bonds  (0, 0)

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

(-) 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 3VLM)

(-) 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 3VLM)

(-) 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:663
 aligned with KATG2_HALMA | O59651 from UniProtKB/Swiss-Prot  Length:731

    Alignment length:700
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728
          KATG2_HALMA    29 SKLNLEILDQNARDVGPVEDDFDYAEEFQKLDLEAVKSDLEELMTSSQDWWPADYGHYGPLFIRMAWHSAGTYRTADGRGGAAGGRQRFAPINSWPDNANLDKARRLLLPIKQKYGQKISWADLMILAGNVAIESMGFKTFGYAGGREDAFEEDKAVNWGPEDEFETQERFDEPGEIQEGLGASVMGLIYVNPEGPDGNPDPEASAKNIRQTFDRMAMNDKETAALIAGGHTFGKVHGADDPEENLGPEPEAAPIEQQGLGWQNKNGNSKGGEMITSGIEGPWTQSPTEWDMGYINNLLDYEWEPEKGPGGAWQWAPKSEELKNSVPDAHDPDEKQTPMMLTTDIALKRDPDYREVMETFQENPMEFGMNFAKAWYKLTHRDMGPPERFLGPEVPDEEMIWQDPLPDADYDLIGDEEIAELKEEILDSDLSVSQLVKTAWASASTYRDSDKRGGANGARLRLEPQKNWEVNEPEQLETVLGTLENIQTEFNDSRSDGTQVSLADLIVLGGNAAVEQAAANAGYDVEIPFEPGRVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDNADLLNLTASELTALIGGMRSIGANYQDTDLGVFTDEPETLTNDFFVNLLDMGTEWEPAADSEHRYKGLDRDTGEVKWEATRIDLIFGSNDRLRAISEVYGSADAEKKLVHDFVDTWSKVMKLDRF 728
               SCOP domains d3vlma1 A:29-423 aut  omated matches                                                                                                                                                                                                                                                                                                                                                                       d3vlma2 A:424-728 automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..........--.hhhhhh..hhhhhhhhhhhhh.............hhhhhhhhhhhhhhh............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........................-----------------------...........hhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...ee............hhhhhhhhhh.....----------.......ee.........hhhhhhhhh..eeeee.....eeeee........ee.......ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.........hhhhh..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--.....hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh................hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh.............hhhhhhhhh..eeeee.......eeeee.....eeeeehhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------------------------------------------------PEROXIDASE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vlm A  29 SKLNLEILDQNARDVGPVED--DYAEEFQKLDLEAVKSDLEELMTSSQDWWPADYGHYGPLFIRMAWHSAGTYRTADGRGGAAGGRQRFAPINSWPDNANLDKARRLLLPIKQKYGQKISWADLMILAGNVAIESMGFKTFGYAGGREDAFEEDKAVNWG-----------------------SVMGLIYVNPEGPDGNPDPEASAKNIRQTFDRAAMNDKETAALIAGGHTFGKVHGADDPEENLGPEPEAAPIEQQGLGWQ----------MITSGIEGPWTQSPTEWDMGYINNLLDYEWEPEKGPGGAWQWAPKSEELKNSVPDAHDPDEKQTPMMLTTDIALKRDPDYREVMETFQENPMEFGMNFAKAWYKLTHRDMGPPERFLGPEVPDEEMIWQDPLPDADYDLIGDEEIAELKEEILDSDLSVSQLVKTAWASASTYRDSDKRGGANGARLRLEPQKNWEVNEPEQLETVLGTLENIQTEFNDS--DGTQVSLADLIVLGGNAAVEQAAANAGYDVEIPFEPGRVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDNADLLNLTASELTALIGGMRSIGANYQDTDLGVFTDEPETLTNDFFVNLLDMGTEWEPAADSEHRYKGLDRDTGEVKWEATRIDLIFGSNDRLRAISEVYGSADAEKKLVHDFVDTWSKVMKLDRF 728
                                    38        48  |     58        68        78        88        98       108       118       128       138       148       158       168       178       188         -         -   |   218       228       238       248       258       268       278       288  |      -   |   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518  |  | 528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728
                                              48 51                                                                                                                                      188                     212                                                                            291        302                                                                                                                                                                                                                        521  |                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         524                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:660
 aligned with KATG2_HALMA | O59651 from UniProtKB/Swiss-Prot  Length:731

    Alignment length:700
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728
          KATG2_HALMA    29 SKLNLEILDQNARDVGPVEDDFDYAEEFQKLDLEAVKSDLEELMTSSQDWWPADYGHYGPLFIRMAWHSAGTYRTADGRGGAAGGRQRFAPINSWPDNANLDKARRLLLPIKQKYGQKISWADLMILAGNVAIESMGFKTFGYAGGREDAFEEDKAVNWGPEDEFETQERFDEPGEIQEGLGASVMGLIYVNPEGPDGNPDPEASAKNIRQTFDRMAMNDKETAALIAGGHTFGKVHGADDPEENLGPEPEAAPIEQQGLGWQNKNGNSKGGEMITSGIEGPWTQSPTEWDMGYINNLLDYEWEPEKGPGGAWQWAPKSEELKNSVPDAHDPDEKQTPMMLTTDIALKRDPDYREVMETFQENPMEFGMNFAKAWYKLTHRDMGPPERFLGPEVPDEEMIWQDPLPDADYDLIGDEEIAELKEEILDSDLSVSQLVKTAWASASTYRDSDKRGGANGARLRLEPQKNWEVNEPEQLETVLGTLENIQTEFNDSRSDGTQVSLADLIVLGGNAAVEQAAANAGYDVEIPFEPGRVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDNADLLNLTASELTALIGGMRSIGANYQDTDLGVFTDEPETLTNDFFVNLLDMGTEWEPAADSEHRYKGLDRDTGEVKWEATRIDLIFGSNDRLRAISEVYGSADAEKKLVHDFVDTWSKVMKLDRF 728
               SCOP domains d3vlmb1 B:29-423 au   tomated matches                                                                                                                                                                                                                                                                                                                                                                      d3vlmb2 B:424-728 automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh......---.hhhhhh..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................---------------------------........hhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..ee....hhhhhh..hhhhhhhhhh.....----------.......ee.........hhhhhhhhhh.eeeee.....eeeee........ee.......ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.........hhhhh..........hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.............hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhh..eehhhhee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh.............hhhhhhhhh..eeeee.......eeeee.....eeeeehhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------------------------------------------------PEROXIDASE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vlm B  29 SKLNLEILDQNARDVGPVE---DYAEEFQKLDLEAVKSDLEELMTSSQDWWPADYGHYGPLFIRMAWHSAGTYRTADGRGGAAGGRQRFAPINSWPDNANLDKARRLLLPIKQKYGQKISWADLMILAGNVAIESMGFKTFGYAGGREDAFEEDKAVNW---------------------------GLIYVNPEGPDGNPDPEASAKNIRQTFDRAAMNDKETAALIAGGHTFGKVHGADDPEENLGPEPEAAPIEQQGLGWQ----------MITSGIEGPWTQSPTEWDMGYINNLLDYEWEPEKGPGGAWQWAPKSEELKNSVPDAHDPDEKQTPMMLTTDIALKRDPDYREVMETFQENPMEFGMNFAKAWYKLTHRDMGPPERFLGPEVPDEEMIWQDPLPDADYDLIGDEEIAELKEEILDSDLSVSQLVKTAWASASTYRDSDKRGGANGARLRLEPQKNWEVNEPEQLETVLGTLENIQTEFNDSRSDGTQVSLADLIVLGGNAAVEQAAANAGYDVEIPFEPGRVDAGPEHTDAPSFDALKPKVDGVRNYIQDDITRPAEEVLVDNADLLNLTASELTALIGGMRSIGANYQDTDLGVFTDEPETLTNDFFVNLLDMGTEWEPAADSEHRYKGLDRDTGEVKWEATRIDLIFGSNDRLRAISEVYGSADAEKKLVHDFVDTWSKVMKLDRF 728
                                    38        |-  |     58        68        78        88        98       108       118       128       138       148       158       168       178        |-         -         -      |218       228       238       248       258       268       278       288  |      -   |   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728
                                             47  51                                                                                                                                     187                         215                                                                         291        302
   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 3VLM)

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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3vlh ARG409LEU VARIANT
3vli CYANIDE ARG409LEU VARIANT
3vlj CYANIDE ARG409LEU VARIANT COMPLEXES WITH O-DIANISIDINE
3vlk SER305ALA VARIANT
3vll SER305ALA VARIANT COMPLEXES WITH INHIBITOR SHA