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(-) Description

Title :  STRUCTURE OF D141A VARIANT OF B. PSEUDOMALLEI KATG
 
Authors :  P. C. Loewen
Date :  11 Aug 16  (Deposition) - 07 Sep 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Catalase-Peroxidase, Katg, D141A Variant, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Vidossich, P. C. Loewen, X. Carpena, I. Fita, C. Rovira
An Ionizable Active-Site Tryptophan Imparts Catalase Activity To A Peroxidase Core.
J. Am. Chem. Soc. V. 136 7249 2014
PubMed: search

(-) 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  (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  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:104 , LEU A:105 , TOX A:111 , PRO A:241 , 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:420 , OXY A:804 , HOH A:962 , HOH A:980 , HOH A:992binding site for residue HEM A 801
02AC2SOFTWAREGLY A:122 , ARG A:123 , GLY A:124 , SER A:494 , HOH A:1026 , HOH A:1490binding site for residue NA A 802
03AC3SOFTWAREGLY A:124 , GLU A:198 , VAL A:200 , HOH A:1490 , HOH A:1541 , HOH A:1629binding site for residue CL A 803
04AC4SOFTWAREARG A:108 , HIS A:112 , ALA A:141 , HEM A:801 , HOH A:920 , HOH A:1158binding site for residue OXY A 804
05AC5SOFTWAREPRO A:154 , HOH A:1423binding site for residue MPD A 805
06AC6SOFTWARETHR A:323binding site for residue MPD A 806
07AC7SOFTWAREHIS A:381 , ARG A:382 , HOH A:932binding site for residue PO4 A 807
08AC8SOFTWAREGLY B:104 , LEU B:105 , TOX B:111 , VAL B:239 , PRO B:241 , 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 , THR B:388 , TRP B:420 , OXY B:804 , HOH B:931 , HOH B:1034 , HOH B:1039binding site for residue HEM B 801
09AC9SOFTWAREGLY B:122 , ARG B:123 , GLY B:124 , SER B:494 , HOH B:992 , HOH B:1515binding site for residue NA B 802
10AD1SOFTWAREGLY B:124 , GLU B:198 , VAL B:200 , HOH B:1515 , HOH B:1558 , HOH B:1638binding site for residue CL B 803
11AD2SOFTWAREARG B:108 , HIS B:112 , ALA B:141 , HEM B:801 , HOH B:905 , HOH B:941binding site for residue OXY B 804
12AD3SOFTWARETHR B:323 , SER B:324binding site for residue MPD B 805
13AD4SOFTWAREHOH B:977binding site for residue MPD B 806
14AD5SOFTWARELYS B:380 , HIS B:381 , ARG B:382binding site for residue PO4 B 807

(-) SS Bonds  (0, 0)

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

(-) 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 5SYH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5SYH)

(-) 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....hhhhhhh.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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh..eehhhhee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhh.............hhhhhhhh...eeeee......eeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5syh A  36 GTSNRDWWPNQLDLSILHRHSSLSDPMGKDFNYAQAFEKLDLAAVKRDLHALMTTSQDWWPADFGHYGGLFIRMAwHSAGTYRTADGRGGAGEGQQRFAPLNSWPANANLDKARRLLWPIKQKYGRAISWADLLILTGNVALESMGFKTFGFAGGRADTWEPEDVYWGSEKIWLELSGGPNSRYSGDRQLENPLAAVQMGLIYVNPEGPDGNPDPVAAARDIRDTFARMAMNDEETVALIAGGHTFGKTHGAGPASNVGAEPEAAGIEAQGLGWKSAYRTGKGADAITSGLEVTWTTTPTQWSHNFFENLFGYEWELTKSPAGAHQWVAKGADAVIPDAFDPSKKHRPTMLTTDLSLRFDPAYEKISRRFHENPEQFADAFARAWFKLTHRDMGPRARYLGPEVPAEVLLWQDPIPAVDHPLIDAADAAELKAKVLASGLTVSQLVSTAWAAASTFRGSDKRGGANGARIRLAPQKDWEANQPEQLAAVLETLEAIRTAFNGAQRGGKQVSLADLIVLAGCAGVEQAAKNAGHAVTVPFAPGRADASQEQTDVESMAVLEPVADGFRNYLKGKYRVPAEVLLVDKAQLLTLSAPEMTVLLGGLRVLGANVGQSRHGVFTAREQALTNDFFVNLLDMGTEWKPTAADADVFEGRDRATGELKWTGTRVDLVFGSHSQLRALAEVYGSADAQEKFVRDFVAVWNKVMNLDRFDLA 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............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
                 5syh B  36 GTSNRDWWPNQLDLSILHRHSSLSDPMGKDFNYAQAFEKLDLAAVKRDLHALMTTSQDWWPADFGHYGGLFIRMAwHSAGTYRTADGRGGAGEGQQRFAPLNSWPANANLDKARRLLWPIKQKYGRAISWADLLILTGNVALESMGFKTFGFAGGRADTWEPEDVYWGSEKIWLELSGGPNSRYSGDRQLENPLAAVQMGLIYVNPEGPDGNPDPVAAARDIRDTFARMAMNDEETVALIAGGHTFGKTHGAGPASNVGAEPEAAGIEAQGLGWKSAYRTGKGADAITSGLEVTWTTTPTQWSHNFFENLFGYEWELTKSPAGAHQWVAKGADAVIPDAFDPSKKHRPTMLTTDLSLRFDPAYEKISRRFHENPEQFADAFARAWFKLTHRDMGPRARYLGPEVPAEVLLWQDPIPAVDHPLIDAADAAELKAKVLASGLTVSQLVSTAWAAASTFRGSDKRGGANGARIRLAPQKDWEANQPEQLAAVLETLEAIRTAFNGAQRGGKQVSLADLIVLAGCAGVEQAAKNAGHAVTVPFAPGRADASQEQTDVESMAVLEPVADGFRNYLKGKYRVPAEVLLVDKAQLLTLSAPEMTVLLGGLRVLGANVGQSRHGVFTAREQALTNDFFVNLLDMGTEWKPTAADADVFEGRDRATGELKWTGTRVDLVFGSHSQLRALAEVYGSADAQEKFVRDFVAVWNKVMNLDRFDLA 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 ; only for superseded entry 4KA5: 1,4)

(no "SCOP Domain" information available for 5SYH, only for superseded entry 4KA5 replaced by 5SYH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:134 - Pro A:135   [ RasMol ]  
    Ala A:508 - Pro A:509   [ RasMol ]  
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    Ala B:508 - Pro B:509   [ RasMol ]  
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  5syh
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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 5sw6 5sx0 5sx1 5sx2 5sx3 5sx6 5sx7 5sxq 5sxr 5sxs 5sxt 5sxw 5sxx 5syi 5syj 5syk 5syl 5syu 5syv 5syw 5syx 5syy 5txq 5v4o 5v53
        KATG_BURPS | Q939D2: 5l02 5l05 5sw4 5sw5 5sw6 5sx0 5sx1 5sx2 5sx3 5sx6 5sx7 5sxq 5sxr 5sxs 5sxt 5sxw 5sxx 5syi 5syk 5syl 5syv 5syx

(-) Related Entries Specified in the PDB File

5l02 5l05 5sw4 5sw5 5sw6 5sx0 5sx1 5sx2 5sx3 5sx6 5sx7 5sxq 5sxr 5sxs 5sxt 5sxx 5syi 5syj 5syk 5syl 5syu 5syv 5syw 5syx 5syy