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(-) Description

Title :  STRUCTURE OF PROTEUS MIRABILIS CATALASE FOR THE NATIVE FORM
 
Authors :  P. Gouet, H. -M. Jouve, O. Dideberg
Date :  24 Jul 02  (Deposition) - 14 Aug 02  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Methionine Sulfone, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Gouet, H. M. Jouve, O. Dideberg
Crystal Structure Of Proteus Mirabilis Pr Catalase With And Without Bound Nadph.
J. Mol. Biol. V. 249 933 1995
PubMed-ID: 7791219  |  Reference-DOI: 10.1006/JMBI.1995.0350

(-) Compounds

Molecule 1 - CATALASE
    Chains: A
    EC Number: 1.11.1.6
    Organism Scientific: PROTEUS MIRABILIS
    Organism Taxid: 584

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OMT1Mod. Amino AcidS-DIOXYMETHIONINE
4SO48Ligand/IonSULFATE ION
Biological Unit 1 (4, 44)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3OMT4Mod. Amino AcidS-DIOXYMETHIONINE
4SO432Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:182 , HIS A:192 , ARG A:216 , HOH A:1405 , HOH A:1493 , HOH A:1494BINDING SITE FOR RESIDUE SO4 A 485
02AC2SOFTWAREARG A:423 , HOH A:1062 , HOH A:1384 , HOH A:1399 , HOH A:1457 , HOH A:1458BINDING SITE FOR RESIDUE SO4 A 486
03AC3SOFTWARESER A:430 , ASP A:432 , ARG A:436BINDING SITE FOR RESIDUE SO4 A 487
04AC4SOFTWAREARG A:182 , ASN A:223 , HOH A:1270BINDING SITE FOR RESIDUE SO4 A 488
05AC5SOFTWAREPRO A:283 , HIS A:284 , ALA A:285 , HOH A:1428BINDING SITE FOR RESIDUE SO4 A 489
06AC6SOFTWAREARG A:216 , GLN A:218 , HOH A:1359BINDING SITE FOR RESIDUE SO4 A 490
07AC7SOFTWAREHOH A:1470BINDING SITE FOR RESIDUE SO4 A 491
08AC8SOFTWAREARG A:45 , ARG A:342 , TYR A:343 , HOH A:1171BINDING SITE FOR RESIDUE SO4 A 492
09AC9SOFTWAREASP A:44 , ARG A:51 , HIS A:54 , ARG A:91 , VAL A:125 , GLY A:126 , ASN A:127 , PHE A:140 , GLY A:195 , SER A:196 , PHE A:313 , MET A:329 , ARG A:333 , SER A:336 , TYR A:337 , HIS A:341 , ARG A:344 , HOH A:1003 , HOH A:1152 , HOH A:1156BINDING SITE FOR RESIDUE HEM A 1001
10BC1SOFTWAREGLU A:38 , HIS A:42 , ARG A:342 , HIS A:349 , HOH A:1103 , HOH A:1135BINDING SITE FOR RESIDUE GOL A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M85)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:383 -Pro A:384

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M85)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CATALASE_2PS00438 Catalase proximal active site signature.CATA_PROMI43-59  1A:43-59
2CATALASE_1PS00437 Catalase proximal heme-ligand signature.CATA_PROMI333-341  1A:333-341
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CATALASE_2PS00438 Catalase proximal active site signature.CATA_PROMI43-59  4A:43-59
2CATALASE_1PS00437 Catalase proximal heme-ligand signature.CATA_PROMI333-341  4A:333-341

(-) Exons   (0, 0)

(no "Exon" information available for 1M85)

(-) 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:476
 aligned with CATA_PROMI | P42321 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:476
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473      
           CATA_PROMI     4 KKLTTAAGAPVVDNNNVITAGPRGPMLLQDVWFLEKLAHFDREVIPERRMHAKGSGAFGTFTVTHDITKYTRAKIFSEVGKKTEMFARFSTVAGERGAADAERDIRGFALKFYTEEGNWDMVGNNTPVFYLRDPLKFPDLNHIVKRDPRTNMRNMAYKWDFFSHLPESLHQLTIDMSDRGLPLSYRFVHGFGSHTYSFINKDNERFWVKFHFRCQQGIKNLMDDEAEALVGKDRESSQRDLFEAIERGDYPRWKLQIQIMPEKEASTVPYNPFDLTKVWPHADYPLMDVGYFELNRNPDNYFSDVEQAAFSPANIVPGISFSPDKMLQGRLFSYGDAHRYRLGVNHHQIPVNAPKCPFHNYHRDGAMRVDGNSGNGITYEPNSGGVFQEQPDFKEPPLSIEGAADHWNHREDEDYFSQPRALYELLSDDEHQRMFARIAGELSQASKETQQRQIDLFTKVHPEYGAGVEKAIKVLE 479
               SCOP domains d1m85a_ A: Catalase I                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Catalase-1m85A02 A:7-391                                                                                                                                                                                                                                                                                                                                                                         -------------------Catalase-rel-1m85A01 A:411-476                                    --- Pfam domains
         Sec.struct. author .............................hhhhhhhhhhhh............eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.ee....eeee.....eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeee.hhhhh...................eeeeeeeeee...hhhhhh.............ee...hhhhhhhhhhhhhhhhhhhh.hhhhh........................................hhhhh.............hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------CATALASE_2       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATALASE_------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m85 A   4 KKLTTAAGAPVVDNNNVITAGPRGPMLLQDVWFLEKLAHFDREVIPERRmHAKGSGAFGTFTVTHDITKYTRAKIFSEVGKKTEMFARFSTVAGERGAADAERDIRGFALKFYTEEGNWDMVGNNTPVFYLRDPLKFPDLNHIVKRDPRTNMRNMAYKWDFFSHLPESLHQLTIDMSDRGLPLSYRFVHGFGSHTYSFINKDNERFWVKFHFRCQQGIKNLMDDEAEALVGKDRESSQRDLFEAIERGDYPRWKLQIQIMPEKEASTVPYNPFDLTKVWPHADYPLMDVGYFELNRNPDNYFSDVEQAAFSPANIVPGISFSPDKMLQGRLFSYGDAHRYRLGVNHHQIPVNAPKCPFHNYHRDGAMRVDGNSGNGITYEPNSGGVFQEQPDFKEPPLSIEGAADHWNHREDEDYFSQPRALYELLSDDEHQRMFARIAGELSQASKETQQRQIDLFTKVHPEYGAGVEKAIKVLE 479
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473      
                                                                            53-OMT
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1M85)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Catalase-rel] (18)
(-)
Clan: no clan defined [family: Catalase] (19)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (CATA_PROMI | P42321)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CATA_PROMI | P42321: 1e93 1h6n 1h7k 1mqf 1nm0 2cag 2cah 3hb6

(-) Related Entries Specified in the PDB File

1e93 1E93 CONTAINS A RECOMBINANT CATALASE DEPLETED IN IRON
2caf 2CAF CONTAINS THE SAME PROTEIN
2cah 2CAH CONTAINS CATALASE FOR THE NATIVE FORM (E-FE(III)) COMPLEXED WITH NADPH