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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALASE-PEROXIDASE FROM SYNECHOCOCCUS PCC 7942
 
Authors :  K. Wada, T. Tada
Date :  28 Mar 03  (Deposition) - 28 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Catalase-Peroxidase, Catalase, Peroxidase, Katg, Synechococcus Pcc 7942, Cyanobacteria, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Wada, T. Tada
Crystal Structure Of Catalase-Peroxidase From Synechococcus Pcc 7942
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CATALASE-PEROXIDASE
    Chains: A
    EC Number: 1.11.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
    Organism Taxid: 1140
    Strain: PCC 7942

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:86 , LEU A:87 , ILE A:89 , ARG A:90 , TRP A:93 , PRO A:224 , LEU A:257 , THR A:258 , GLY A:261 , HIS A:262 , GLY A:265 , LYS A:266 , CYS A:267 , HIS A:268 , THR A:306 , SER A:307 , TRP A:313 , ALA A:374 , PHE A:402 , TRP A:406 , HOH A:742 , HOH A:743 , HOH A:769BINDING SITE FOR RESIDUE HEM A 721

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UB2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:116 -Pro A:117
2Ala A:490 -Pro A:491

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UB2)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.KATG_SYNE786-97  1A:85-96
2PEROXIDASE_4PS50873 Plant heme peroxidase family profile.KATG_SYNE7455-720  1A:455-720
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.KATG_SYNE786-97  2A:85-96
2PEROXIDASE_4PS50873 Plant heme peroxidase family profile.KATG_SYNE7455-720  2A:455-720

(-) Exons   (0, 0)

(no "Exon" information available for 1UB2)

(-) 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:700
 aligned with KATG_SYNE7 | Q31MN3 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:701
                                                                                                                                                                                                                                                                                                                                                330                                                                                                                                                                                                                                                                                                                                                                                                      
                                                                                                                                                                                                                                                                                                                                              329 |                                                                                                                                                                                                                                                                                                                                                                                                      
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           KATG_SYNE7    21 STAEWWPKALNLDILSQHDRKTNPMGPDFNYQEEVKKLDVAALKQDLQALMTDSQDWWPADWGHYGGLMIRLTWHAAGTYRIADGRGGAGTGNQRFAPLNSWPDNTNLDKARRLLWPIKQKYGNKLSWADLIAYAGTIAYESMGLKTFGFAFGREDIWHPEKDIYWGPEKEWVPPSTNPNSRYTGDRELENPLAAVTMGLIYVNPEGVDGNPDPLKTAHDVRVTFARMAMNDEETVALTAGGHTVGKCHGNGNAALLGPEPEGADVEDQGLGWINKTQSGIGRNAVTSGLEGAWTPHPTQWDNGYFRML-LNYDWELKKSPAGAWQWEPINPREEDLPVDVEDPSIRRNLVMTDADMAMKMDPEYRKISERFYQDPAYFADVFARAWFKLTHRDMGPKARYIGPDVPQEDLIWQDPIPAGNRNYDVQAVKDRIAASGLSISELVSTAWDSARTYRNSDKRGGANGARIRLAPQKDWEGNEPDRLAKVLAVLEGIAAATGASVADVIVLAGNVGVEQAARAAGVEIVLPFAPGRGDATAEQTDTESFAVLEPIHDGYRNWLKQDYAATPEELLLDRTQLLGLTAPEMTVLIGGLRVLGTNHGGTKHGVFTDREGVLTNDFFVNLTDMNYLWKPAGKNLYEICDRKTNQVKWTATRVDLVFGSNSILRAYSELYAQDDNKEKFVRDFVAAWTKVMNADRFDLD 720
               SCOP domains d1ub2a1 A:21-426 Catalase-peroxidase Ka tG                                                                                                                                                                                                                                                                                                                                                                             d1ub2a2 A:427-720 Catalase-peroxidase KatG                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ub2A01 A:21-185,A:394-428  [code=1.10. 520.10, no name defined]                                                                                                      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1ub2A01 A:21-185,A:394-428         1ub2A03 A:429-573,A:696-720  [code=1.10.520.10, no name defined]                                                                                 1ub2A04 A:574-695 Peroxidase, domain 2                                                                                    1ub2A03                   CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------peroxidase-1ub2A01 A:399-694                                                                                                                                                                                                                                                                            -------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------peroxidase-1ub2A02 A:399-694                                                                                                                                                                                                                                                                            -------------------------- Pfam domains (2)
         Sec.struct. author ..........hhhhhh.............hhhhhhh...-..hhhhhhhhh........hhhhhhhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................................ee...ee.................hhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...............hhhhhhhhhh...........hhhhh.............................eeeee.....eeeee...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhhhh..........hhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh........................hhhhh..eehhhhee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhh.............hhhhhhhh...eeeee.....eeeee.....eeeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEROXIDASE_4  PDB: A:455-720 UniProt: 455-720                                                                                                                                                                                                                              PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ub2 A  21 STAEWWPKALNLDILSQHDRKTNPMGPDFNYQEEVQKLD-AALKQDLQALMTDSQDWWPADWGHYGGLMIRLTWHAAGTYRIADGRGGAGTGNQRFAPLNSWPDNTNLDKARRLLWPIKQKYGNKLSWADLIAYAGTIAYESMGLKTFGFAFGREDIWHPEKDIYWGPEKEWFPPSTNPNSRYTGDRELENPLAAVTMGLIYVNPEGVDGNPDPLKTAHDVRVTFARMAMNDEETVALTAGGHTVGKCHGNGNAALLGPEPEGADVEDQGLGWINKTQSGIGRNAVTSGLEGAWTPHPTQWDNGYFAVCSLNYDWELKKNPAGAWQWEPINPREEDLPVDVEDPSIRRNLVMTDADMAMKMDPEYRKISERFYQDPAYFADVFARAWFKLTHRDMGPKARYIGPDVPQEDLIWQDPIPAGNRNYDVQAVKDRIAASGLSISELVSTAWDSARTYRNSDKRGGANGARIRLAPQKDWEGNEPDRLPKVLAVLEGISAATGATVADVIVLAGNVGVEQKARAAGVEIVLPFAPGRGDATAEQTDTESFAVLEPIHDAIATGSSRTMRQRLKNCCLIATQLLGLTAPEMTVLIGGLRVLGTNHGGTKHVVFTDREGVLTNDFFVNLTDMNYLWKPAGKNLYEICDRKTNQVKWTATRVDLVFGSNSILRAYSELYAQDDNKEKFVRDFVAAWTKVMNADRFDLD 720
                                    30        40        50        |-|       69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719 
                                                                 59 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                   60
   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, 2)

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

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: peroxidase] (92)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (KATG_SYNE7 | Q31MN3)
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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        KATG_SYNE7 | Q31MN3: 3wnu 3wxo 3x16 4pae

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