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(-) Description

Title :  CRYSTAL STRUCTURE OF AN OXOFERRYL SPECIES OF CATALASE-PEROXIDASE KATG AT PH5.6
 
Authors :  P. C. Loewen
Date :  08 Aug 16  (Deposition) - 24 Aug 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Catalase-Peroxidase, Katg, Compound I, Oxoferryl Species, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Carpena, B. Wiseman, T. Deemagarn, R. Singh, J. Switala, A. Ivancich, I. Fita, P. C. Loewen
A Molecular Switch And Electronic Circuit Modulate Catalase Activity In Catalase-Peroxidases.
Embo Rep. V. 6 1156 2005
PubMed-ID: 16211084

(-) Compounds

Molecule 1 - CATALASE-PEROXIDASE
    Chains: A, B
    EC Number: 1.11.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: KATG, BURPS1710B_3366
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI (STRAIN 1710B)
    Organism Taxid: 320372
    Strain: 1710B
    Synonym: CP,PEROXIDASE/CATALASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric/Biological Unit (6, 14)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NA2Ligand/IonSODIUM ION
4O2Ligand/IonOXYGEN ATOM
5OXY3Ligand/IonOXYGEN MOLECULE
6PO42Ligand/IonPHOSPHATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:104 , LEU A:105 , TRP A:111 , LEU A:274 , ILE A:275 , GLY A:278 , HIS A:279 , GLY A:282 , LYS A:283 , THR A:284 , HIS A:285 , THR A:323 , SER A:324 , TRP A:330 , THR A:388 , TRP A:420 , OXY A:803 , OXY A:804 , O A:806 , HOH A:934 , HOH A:1040 , HOH A:1079binding site for residue HEM A 801
02AC2SOFTWAREGLY A:122 , ARG A:123 , GLY A:124 , SER A:494 , HOH A:919 , HOH A:1097binding site for residue NA A 802
03AC3SOFTWAREARG A:108 , HIS A:112 , ASP A:141 , HEM A:801 , OXY A:804 , O A:806 , HOH A:902binding site for residue OXY A 803
04AC4SOFTWARETRP A:111 , HIS A:112 , HEM A:801 , OXY A:803 , O A:806 , HOH A:1188 , HOH A:1312binding site for residue OXY A 804
05AC5SOFTWARELYS A:380 , HIS A:381 , ARG A:382 , HOH A:1243binding site for residue PO4 A 805
06AC6SOFTWARETRP A:111 , HIS A:112 , HEM A:801 , OXY A:803 , OXY A:804binding site for residue O A 806
07AC7SOFTWARETHR A:323 , SER A:324binding site for residue MPD A 807
08AC8SOFTWAREASP A:83 , PRO A:154 , HOH A:1126 , HOH A:1392binding site for residue MPD A 808
09AC9SOFTWAREGLY B:104 , LEU B:105 , TRP B:111 , LEU B:274 , ILE B:275 , GLY B:278 , HIS B:279 , GLY B:282 , LYS B:283 , THR B:284 , HIS B:285 , THR B:323 , SER B:324 , TRP B:330 , THR B:388 , TRP B:420 , O B:803 , OXY B:804 , HOH B:946 , HOH B:969 , HOH B:1086binding site for residue HEM B 801
10AD1SOFTWAREGLY B:122 , ARG B:123 , GLY B:124 , SER B:494 , HOH B:945 , HOH B:1078binding site for residue NA B 802
11AD2SOFTWARETRP B:111 , HIS B:112 , HEM B:801 , OXY B:804 , HOH B:973binding site for residue O B 803
12AD3SOFTWAREARG B:108 , HIS B:112 , HEM B:801 , O B:803 , HOH B:904binding site for residue OXY B 804
13AD4SOFTWAREHIS B:381 , ARG B:382 , HOH B:902binding site for residue PO4 B 805
14AD5SOFTWAREALA B:290 , THR B:323 , SER B:324binding site for residue MPD B 806

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5SW6)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ala A:134 -Pro A:135
2Asn A:227 -Pro A:228
3Ala A:508 -Pro A:509
4Ala B:134 -Pro B:135
5Asn B:227 -Pro B:228
6Ala B:508 -Pro B:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5SW6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5SW6)

(-) Exons   (0, 0)

(no "Exon" information available for 5SW6)

(-) 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:713
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhh..hhhhh......hhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................................ee...ee.................hhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.........hhhhh..hhhhhhhhhh...........hhhhh.................hhhhhhhhhh.eeeee.....eeeee......ee.......ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhh..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh..eehhhhee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh.............hhhhhhhh...eeeee......eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5sw6 A  36 GTSNRDWWPNQLDLSILHRHSSLSDPMGKDFNYAQAFEKLDLAAVKRDLHALMTTSQDWWPADFGHYGGLFIRMAWHSAGTYRTADGRGGAGEGQQRFAPLNSWPDNANLDKARRLLWPIKQKYGRAISWADLLILTGNVALESMGFKTFGFAGGRADTWEPEDVYWGSEKIWLELSGGPNSRYSGDRQLENPLAAVQMGLIYVNPEGPDGNPDPVAAARDIRDTFARMAMNDEETVALIAGGHTFGKTHGAGPASNVGAEPEAAGIEAQGLGWKSAYRTGKGADAITSGLEVTWTTTPTQWSHNFFENLFGYEWELTKSPAGAHQWVAKGADAVIPDAFDPSKKHRPTMLTTDLSLRFDPAYEKISRRFHENPEQFADAFARAWFKLTHRDMGPRARYLGPEVPAEVLLWQDPIPAVDHPLIDAADAAELKAKVLASGLTVSQLVSTAWAAASTFRGSDKRGGANGARIRLAPQKDWEANQPEQLAAVLETLEAIRTAFNGAQRGGKQVSLADLIVLAGCAGVEQAAKNAGHAVTVPFAPGRADASQEQTDVESMAVLEPVADGFRNYLKGKYRVPAEVLLVDKAQLLTLSAPEMTVLLGGLRVLGANVGQSRHGVFTAREQALTNDFFVNLLDMGTEWKPTAADADVFEGRDRATGELKWTGTRVDLVFGSHSQLRALAEVYGSADAQEKFVRDFVAVWNKVMNLDRFDLA 748
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745   


Chain B from PDB  Type:PROTEIN  Length:713
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhh..hhhhh......hhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................................ee...ee.................hhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........hhhhh..hhhhhhhhhh...........hhhhh.................hhhhhhhhhh.eeeee.....eeeee......ee.......ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhh..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhh..eehhhhee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh.............hhhhhhhh...eeeee......eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5sw6 B  36 GTSNRDWWPNQLDLSILHRHSSLSDPMGKDFNYAQAFEKLDLAAVKRDLHALMTTSQDWWPADFGHYGGLFIRMAWHSAGTYRTADGRGGAGEGQQRFAPLNSWPDNANLDKARRLLWPIKQKYGRAISWADLLILTGNVALESMGFKTFGFAGGRADTWEPEDVYWGSEKIWLELSGGPNSRYSGDRQLENPLAAVQMGLIYVNPEGPDGNPDPVAAARDIRDTFARMAMNDEETVALIAGGHTFGKTHGAGPASNVGAEPEAAGIEAQGLGWKSAYRTGKGADAITSGLEVTWTTTPTQWSHNFFENLFGYEWELTKSPAGAHQWVAKGADAVIPDAFDPSKKHRPTMLTTDLSLRFDPAYEKISRRFHENPEQFADAFARAWFKLTHRDMGPRARYLGPEVPAEVLLWQDPIPAVDHPLIDAADAAELKAKVLASGLTVSQLVSTAWAAASTFRGSDKRGGANGARIRLAPQKDWEANQPEQLAAVLETLEAIRTAFNGAQRGGKQVSLADLIVLAGCAGVEQAAKNAGHAVTVPFAPGRADASQEQTDVESMAVLEPVADGFRNYLKGKYRVPAEVLLVDKAQLLTLSAPEMTVLLGGLRVLGANVGQSRHGVFTAREQALTNDFFVNLLDMGTEWKPTAADADVFEGRDRATGELKWTGTRVDLVFGSHSQLRALAEVYGSADAQEKFVRDFVAVWNKVMNLDRFDLA 748
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745
   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 ; only for superseded entry 2B2R: 1,4)

(no "SCOP Domain" information available for 5SW6, only for superseded entry 2B2R replaced by 5SW6)

(-) CATH Domains  (0, 0 ; only for superseded entry 2B2R: 2,6)

(no "CATH Domain" information available for 5SW6, only for superseded entry 2B2R replaced by 5SW6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5SW6)

(-) Gene Ontology  (9, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Ala A:508 - Pro A:509   [ RasMol ]  
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    Ala B:508 - Pro B:509   [ RasMol ]  
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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
        KATG_BURP1 | Q3JNW6: 5kq0 5kq2 5kq3 5kq6 5kqh 5kqi 5kqk 5kqn 5kqq 5ksf 5ksg 5ksk 5ksn 5kt8 5kt9 5l02 5l05 5sw4 5sw5 5sx0 5sx1 5sx2 5sx3 5sx6 5sx7 5sxq 5sxr 5sxs 5sxt 5sxw 5sxx 5syh 5syi 5syj 5syk 5syl 5syu 5syv 5syw 5syx 5syy 5txq 5v4o 5v53
        KATG_BURPS | Q939D2: 5l02 5l05 5sw4 5sw5 5sx0 5sx1 5sx2 5sx3 5sx6 5sx7 5sxq 5sxr 5sxs 5sxt 5sxw 5sxx 5syh 5syi 5syk 5syl 5syv 5syx

(-) Related Entries Specified in the PDB File

5l02 5l05 5sw4 5sw5 5sx0 5sx1 5sx2 5sx3 5sx6 5sx7 5sxq 5sxr 5sxs 5sxt 5sxx 5syh 5syi 5syj 5syk 5syl 5syu 5syv 5syw 5syx 5syy