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(-) Description

Title :  CRYSTAL STRUCTURE OF THE D141A/Q233E VARIANT OF CATALASE-PEROXIDASE FROM B. PSEUDOMALLEI
 
Authors :  P. C. Loewen
Date :  05 Jul 16  (Deposition) - 26 Apr 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Catalase, Peroxidase, D141A, Q233E, Heme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Machuqueiro, B. Victor, J. Switala, J. Villanueva, C. Rovira, I. Fita, P. C. Loewen
The Catalase Activity Of Catalase-Peroxidases Is Modulated By Changes In The Pka Of The Distal Histidine.
Biochemistry V. 56 2271 2017
PubMed-ID: 28409923  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B01276

(-) Compounds

Molecule 1 - CATALASE-PEROXIDASE
    Chains: A, B
    EC Number: 1.11.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKS
    Expression System Strain: UM262
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: KATG, BURPS1710B_3366
    Mutation: YES
    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  (7, 16)

Asymmetric/Biological Unit (7, 16)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4NA2Ligand/IonSODIUM ION
5OXY2Ligand/IonOXYGEN MOLECULE
6PO42Ligand/IonPHOSPHATE ION
7TOX2Mod. Amino Acid1-HYDROPEROXY-L-TRYPTOPHAN

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:104 , LEU A:105 , TOX A:111 , VAL A:239 , LEU A:274 , 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 , OXY A:804 , HOH A:984 , HOH A:997 , HOH A:1040binding site for residue HEM A 801
02AC2SOFTWAREGLY A:122 , ARG A:123 , GLY A:124 , SER A:494 , HOH A:949 , HOH A:1384binding site for residue NA A 802
03AC3SOFTWAREGLY A:124 , GLU A:198 , VAL A:200 , HOH A:1384binding site for residue CL A 803
04AC4SOFTWAREARG A:108 , TOX A:111 , HIS A:112 , ALA A:141 , HEM A:801 , HOH A:922binding site for residue OXY A 804
05AC5SOFTWAREHIS A:381 , ARG A:382 , HOH A:1062binding site for residue PO4 A 805
06AC6SOFTWARELEU A:209 , THR A:323 , SER A:324binding site for residue MPD A 806
07AC7SOFTWAREASP A:83 , PRO A:154 , HOH A:1226 , HOH A:1289binding site for residue MPD A 807
08AC8SOFTWAREASP A:663 , VAL A:666 , HOH A:1274 , HOH A:1355 , HOH A:1369binding site for residue MPD A 808
09AC9SOFTWAREGLY B:104 , LEU B:105 , ILE B:107 , TOX B:111 , VAL B:239 , LEU B:274 , GLY B:278 , HIS B:279 , GLY B:282 , LYS B:283 , THR B:284 , HIS B:285 , THR B:323 , SER B:324 , THR B:388 , TRP B:420 , OXY B:804 , HOH B:941 , HOH B:1004 , HOH B:1052binding site for residue HEM B 801
10AD1SOFTWAREGLY B:122 , ARG B:123 , GLY B:124 , SER B:494 , HOH B:1101 , HOH B:1138binding site for residue NA B 802
11AD2SOFTWAREARG B:108 , TOX B:111 , HIS B:112 , ALA B:141 , HEM B:801 , HOH B:912binding site for residue OXY B 804
12AD3SOFTWARELYS B:380 , HIS B:381 , ARG B:382binding site for residue PO4 B 805
13AD4SOFTWARETHR B:323 , SER B:324binding site for residue MPD B 806

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KQ3)

(-) 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 5KQ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KQ3)

(-) Exons   (0, 0)

(no "Exon" information available for 5KQ3)

(-) 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..eeee.....eeee.......ee.......ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhh..........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhh..eehhhhee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh.............hhhhhhhh...eeeee......eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq3 A  36 GTSNRDWWPNQLDLSILHRHSSLSDPMGKDFNYAQAFEKLDLAAVKRDLHALMTTSQDWWPADFGHYGGLFIRMAwHSAGTYRTADGRGGAGEGQQRFAPLNSWPANANLDKARRLLWPIKQKYGRAISWADLLILTGNVALESMGFKTFGFAGGRADTWEPEDVYWGSEKIWLELSGGPNSRYSGDRQLENPLAAVEMGLIYVNPEGPDGNPDPVAAARDIRDTFARMAMNDEETVALIAGGHTFGKTHGAGPASNVGAEPEAAGIEAQGLGWKSAYRTGKGADAITSGLEVTWTTTPTQWSHNFFENLFGYEWELTKSPAGAHQWVAKGADAVIPDAFDPSKKHRPTMLTTDLSLRFDPAYEKISRRFHENPEQFADAFARAWFKLTHRDMGPRARYLGPEVPAEVLLWQDPIPAVDHPLIDAADAAELKAKVLASGLTVSQLVSTAWAAASTFRGSDKRGGANGARIRLAPQKDWEANQPEQLAAVLETLEAIRTAFNGAQRGGKQVSLADLIVLAGCAGVEQAAKNAGHAVTVPFAPGRADASQEQTDVESMAVLEPVADGFRNYLKGKYRVPAEVLLVDKAQLLTLSAPEMTVLLGGLRVLGANVGQSRHGVFTAREQALTNDFFVNLLDMGTEWKPTAADADVFEGRDRATGELKWTGTRVDLVFGSHSQLRALAEVYGSADAQEKFVRDFVAVWNKVMNLDRFDLA 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   
                                                                                                     111-TOX                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:713
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................................ee...ee.................hhhhh.hhhhhhhhhhhhhhh...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...hhhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq3 B  36 GTSNRDWWPNQLDLSILHRHSSLSDPMGKDFNYAQAFEKLDLAAVKRDLHALMTTSQDWWPADFGHYGGLFIRMAwHSAGTYRTADGRGGAGEGQQRFAPLNSWPANANLDKARRLLWPIKQKYGRAISWADLLILTGNVALESMGFKTFGFAGGRADTWEPEDVYWGSEKIWLELSGGPNSRYSGDRQLENPLAAVEMGLIYVNPEGPDGNPDPVAAARDIRDTFARMAMNDEETVALIAGGHTFGKTHGAGPASNVGAEPEAAGIEAQGLGWKSAYRTGKGADAITSGLEVTWTTTPTQWSHNFFENLFGYEWELTKSPAGAHQWVAKGADAVIPDAFDPSKKHRPTMLTTDLSLRFDPAYEKISRRFHENPEQFADAFARAWFKLTHRDMGPRARYLGPEVPAEVLLWQDPIPAVDHPLIDAADAAELKAKVLASGLTVSQLVSTAWAAASTFRGSDKRGGANGARIRLAPQKDWEANQPEQLAAVLETLEAIRTAFNGAQRGGKQVSLADLIVLAGCAGVEQAAKNAGHAVTVPFAPGRADASQEQTDVESMAVLEPVADGFRNYLKGKYRVPAEVLLVDKAQLLTLSAPEMTVLLGGLRVLGANVGQSRHGVFTAREQALTNDFFVNLLDMGTEWKPTAADADVFEGRDRATGELKWTGTRVDLVFGSHSQLRALAEVYGSADAQEKFVRDFVAVWNKVMNLDRFDLA 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   
                                                                                                     111-TOX
   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 5KQ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KQ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KQ3)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ala B:508 - Pro B:509   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        KATG_BURP1 | Q3JNW6: 5kq0 5kq2 5kq6 5kqh 5kqi 5kqk 5kqn 5kqq 5ksf 5ksg 5ksk 5ksn 5kt8 5kt9 5l02 5l05 5sw4 5sw5 5sw6 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

(-) Related Entries Specified in the PDB File

5kq0 5kq2 5kq6 5kq7 5kqh 5kqi 5kqk 5kqn 5kqq