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(-) Description

Title :  COMPOUND II STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE
 
Authors :  G. N. Murshudov, A. I. Grebenko, J. A. Brannigan, A. A. Antson, V. V. Barynin, G. G. Dodson, Z. Dauter, K. S. Wilson, W. R. Melik-Adamyan
Date :  15 Mar 02  (Deposition) - 26 Apr 02  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Oxidoreductase, Catalase, Hydrogen Peroxide Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. N. Murshudov, A. I. Grebenko, J. A. Brannigan, A. A. Antson, V. V. Barynin, G. G. Dodson, Z. Dauter, K. S. Wilson, W. R. Melik-Adamyan
The Structures Of Micrococcus Lysodeikticus Catalase, Its Ferryl Intermediate (Compound Ii) And Nadph Complex.
Acta Crystallogr. , Sect. D V. 58 1972 2002
PubMed-ID: 12454454  |  Reference-DOI: 10.1107/S0907444902016566

(-) Compounds

Molecule 1 - CATALASE
    Chains: A
    EC Number: 1.11.1.6
    Organism Scientific: MICROCOCCUS LUTEUS
    Organism Taxid: 1270

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3O1Ligand/IonOXYGEN ATOM
4SME5Mod. Amino AcidMETHIONINE SULFOXIDE
5SO43Ligand/IonSULFATE ION
Biological Unit 1 (4, 44)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3O-1Ligand/IonOXYGEN ATOM
4SME20Mod. Amino AcidMETHIONINE SULFOXIDE
5SO412Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:188 , ASN A:198 , TYR A:200 , ARG A:295 , HOH A:2249 , HOH A:2607 , HOH A:2608BINDING SITE FOR RESIDUE SO4 A 505
2AC2SOFTWAREVAL A:101 , ASP A:113 , PHE A:139 , PHE A:149 , GLN A:153 , HOH A:2195 , HOH A:2610BINDING SITE FOR RESIDUE ACT A 506
3AC3SOFTWAREARG A:112 , GLN A:167 , LEU A:184 , SME A:185 , VAL A:495 , HOH A:2195 , HOH A:2215 , HOH A:2611BINDING SITE FOR RESIDUE ACT A 507
4AC4SOFTWAREARG A:59 , GLU A:104 , LYS A:154 , ARG A:155 , GLU A:373 , HOH A:2135 , HOH A:2613 , HOH A:2614 , HOH A:2615 , HOH A:2616BINDING SITE FOR RESIDUE SO4 A 508
5AC5SOFTWAREARG A:25 , HOH A:2182 , HOH A:2619 , HOH A:2620 , HOH A:2622 , HOH A:2623BINDING SITE FOR RESIDUE SO4 A 509
6AC6SOFTWAREHIS A:47 , ASN A:51 , ARG A:58 , ARG A:59 , HIS A:61 , ARG A:97 , GLY A:116 , VAL A:131 , GLY A:132 , ASN A:133 , PRO A:143 , PHE A:146 , GLY A:201 , SER A:202 , LEU A:284 , PHE A:319 , MET A:335 , ARG A:339 , TYR A:343 , GLN A:347 , ARG A:350 , O A:600 , HOH A:2127 , HOH A:2604 , HOH A:2605BINDING SITE FOR RESIDUE HEM A 504
7AC7SOFTWAREPRO A:60 , HIS A:61 , PHE A:146 , HEM A:504BINDING SITE FOR RESIDUE O A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:59 -Pro A:60
2Val A:388 -Pro A:389

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CATALASE_3PS51402 catalase family profile.CATA_MICLU10-490  1A:10-490
2CATALASE_2PS00438 Catalase proximal active site signature.CATA_MICLU50-66  1A:50-66
3CATALASE_1PS00437 Catalase proximal heme-ligand signature.CATA_MICLU339-347  1A:339-347
Biological Unit 1 (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CATALASE_3PS51402 catalase family profile.CATA_MICLU10-490  4A:10-490
2CATALASE_2PS00438 Catalase proximal active site signature.CATA_MICLU50-66  4A:50-66
3CATALASE_1PS00437 Catalase proximal heme-ligand signature.CATA_MICLU339-347  4A:339-347

(-) Exons   (0, 0)

(no "Exon" information available for 1GWF)

(-) 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:498
 aligned with CATA_MICLU | P29422 from UniProtKB/Swiss-Prot  Length:503

    Alignment length:498
                                    15        25        35        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        
           CATA_MICLU     6 TTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERRPHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFALRFYTEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAHQVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIAGENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVGTLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLPVNRPKNAVHNYAFEGQMWYDHTGDRSTYVPNSNGDSWSDETGPVDDGWEADGTLTREAQALRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQRIEDEVKRHEGDGIPGVEAGGEARM 503
               SCOP domains d1gwfa_ A: Catalase I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................................hhhhhhhhhhhh............eeeeeeeeee.........hhhhh...eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.ee.............eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeee.hhhhhh..................eeeeeeeeee...hhhhhh..................hhhhhhhhhhhhhhhhhhh..hhhhhhhhh................................................................hhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----CATALASE_3  PDB: A:10-490 UniProt: 10-490                                                                                                                                                                                                                                                                                                                                                                                                                                                        ------------- PROSITE (1)
                PROSITE (2) --------------------------------------------CATALASE_2       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATALASE_------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gwf A   6 TTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRmNIPERRPHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFALRFYTEEGNYDLVGNNTPIFFLRDPmKFTHFIRSQKRLPDSGLRDATmQWDFWTNNPESAHQVTYLmGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIAGENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVGTLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLPVNRPKNAVHNYAFEGQmWYDHTGDRSTYVPNSNGDSWSDETGPVDDGWEADGTLTREAQALRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQRIEDEVKRHEGDGIPGVEAGGEARI 503
                                    15        25        35        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        
                                                                          53-SME                                                                                    144-SME               166-SME            185-SME                                                                                                                                                                                        376-SME
   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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GWF)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (CATA_MICLU | P29422)
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_MICLU | P29422: 1gwe 1gwh 1hbz

(-) Related Entries Specified in the PDB File

1gwe ATOMIC RESOLUTION STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE
1gwh ATOMIC RESOLUTION STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE COMPLEXED WITH NADPH