1GWE - JenaLib

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Title :   ATOMIC RESOLUTION 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) - 15 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.88

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Oxidoreductase, Catalase, Hdyrogen-Peroxide: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

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:188 , ASN A:198 , TYR A:200 , ARG A:295 , HOH A:2854 , HOH A:2857 , HOH A:2858 , HOH A:2861	BINDING SITE FOR RESIDUE SO4 A 505
2	AC2	SOFTWARE	ARG A:25 , ASN A:173 , PRO A:175 , HOH A:2341 , HOH A:2862 , HOH A:2863 , HOH A:2866 , HOH A:2867 , HOH A:2868 , HOH A:2869	BINDING SITE FOR RESIDUE SO4 A 506
3	AC3	SOFTWARE	ARG A:59 , GLU A:104 , LYS A:154 , ARG A:155 , GLU A:373 , HOH A:2104 , HOH A:2294 , HOH A:2870 , HOH A:2871 , HOH A:2872 , HOH A:2873 , HOH A:2874 , HOH A:2875 , HOH A:2876 , HOH A:2877 , HOH A:2878	BINDING SITE FOR RESIDUE SO4 A 507
4	AC4	SOFTWARE	HIS A:47 , ASN A:51 , ARG A:58 , ARG A:59 , PRO A:60 , HIS A:61 , ARG A:97 , GLY A:116 , ALA A:118 , 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 , HOH A:2185 , HOH A:2850 , HOH A:2851 , HOH A:2852 , HOH A:2853	BINDING SITE FOR RESIDUE HEM A 504

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

Asymmetric Unit

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

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

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CATALASE_3	PS51402	catalase family profile.	CATA_MICLU	10-490	1	A:10-490
2	CATALASE_2	PS00438	Catalase proximal active site signature.	CATA_MICLU	50-66	1	A:50-66
3	CATALASE_1	PS00437	Catalase proximal heme-ligand signature.	CATA_MICLU	339-347	1	A:339-347

Biological Unit 1 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CATALASE_3	PS51402	catalase family profile.	CATA_MICLU	10-490	4	A:10-490
2	CATALASE_2	PS00438	Catalase proximal active site signature.	CATA_MICLU	50-66	4	A:50-66
3	CATALASE_1	PS00437	Catalase proximal heme-ligand signature.	CATA_MICLU	339-347	4	A:339-347

(no "Exon" information available for 1GWE)

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
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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 d1gwea_ A: Catalase I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................................hhhhhhhhhhhh............eeeeeeeeee.........hhhhh...eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..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
                 1gwe 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

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Heme-dependent catalase-like (82)

Superfamily: Heme-dependent catalase-like (82)

Family: Heme-dependent catalases (80)

Protein domain: Catalase I (32)

Micrococcus lysodeikticus [TaxId: 1270] (4)

d1gwea_

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

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

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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	Cis Peptide Bonds
		Arg A:59 - Pro A:60	[ RasMol ]
		Val A:388 - Pro A:389	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1gwe
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	CATA_MICLU \| P29422
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	1.11.1.6
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	CATA_MICLU \| P29422	:	1gwf 1gwh 1hbz

1gwf	COMPOUND II STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE
1gwh	ATOMIC RESOLUTION STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE COMPLEXED WITH NADPH

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (10, 10)

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