3WNU - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF CATALASE-PEROXIDASE, KATG, FROM SYNECHOCOCCUS PCC7942

Authors :   T. Tada, K. Wada, S. Kamachi

Date :   17 Dec 13 (Deposition) - 12 Mar 14 (Release) - 12 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Peroxidase Family, Peroxidase/Catalase Subfamily, Oxidoreductase, Heme B, Fe, Cross-Link, Covalent Trp-Tyr-Met Adduct (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kamachi, K. Wada, M. Tamoi, S. Shigeoka, T. Tada
The 2. 2 Aa Resolution Structure Of The Catalase-Peroxidase Katg From Synechococcus Elongatus Pcc7942.
Acta Crystallogr. , Sect. F V. 70 288 2014
PubMed: search | Reference-DOI: 10.1107/S2053230X14002052

Molecule 1 - CATALASE-PEROXIDASE
	Chains	:	A
	EC Number	:	1.11.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALASE-PEROXIDASE
	Gene	:	KATG, SYNPCC7942_1656
	Organism Scientific	:	SYNECHOCOCCUS ELONGATUS
	Organism Taxid	:	1140
	Strain	:	PCC 7942
	Synonym	:	CP, PEROXIDASE/CATALASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	HEB	1	Ligand/Ion	HEME B/C
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	HEB	2	Ligand/Ion	HEME B/C
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:87 , LEU A:88 , ILE A:90 , ARG A:91 , TRP A:94 , PHE A:245 , LEU A:258 , THR A:259 , GLY A:262 , HIS A:263 , GLY A:266 , LYS A:267 , CYS A:268 , HIS A:269 , THR A:307 , SER A:308 , TRP A:314 , TRP A:406 , HOH A:915 , HOH A:943 , HOH A:978	BINDING SITE FOR RESIDUE HEB A 801
2	AC2	SOFTWARE	GLY A:105 , ARG A:106 , GLY A:107 , SER A:476 , HOH A:1078 , HOH A:1325	BINDING SITE FOR RESIDUE NA A 802
3	AC3	SOFTWARE	THR A:264 , THR A:315 , HIS A:317 , GLN A:320 , ASP A:322	BINDING SITE FOR RESIDUE NA A 803

(no "SS Bond" information available for 3WNU)

Asymmetric Unit

No.	Residues
1	Ala A:117	-	Pro A:118
2	Ala A:490	-	Pro A:491

(no "SAP(SNP)/Variant" information available for 3WNU)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	KATG_SYNE7	86-97	1	A:86-97
2	PEROXIDASE_4	PS50873	Plant heme peroxidase family profile.	KATG_SYNE7	455-720	1	A:455-720

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	KATG_SYNE7	86-97	2	A:86-97
2	PEROXIDASE_4	PS50873	Plant heme peroxidase family profile.	KATG_SYNE7	455-720	2	A:455-720

(no "Exon" information available for 3WNU)

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:710
 aligned with KATG_SYNE7 | Q31MN3 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:710
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720
           KATG_SYNE7    11 MHGGATTVNISTAEWWPKALNLDILSQHDRKTNPMGPDFNYQEEVKKLDVAALKQDLQALMTDSQDWWPADWGHYGGLMIRLTWHAAGTYRIADGRGGAGTGNQRFAPLNSWPDNTNLDKARRLLWPIKQKYGNKLSWADLIAYAGTIAYESMGLKTFGFAFGREDIWHPEKDIYWGPEKEWVPPSTNPNSRYTGDRELENPLAAVTMGLIYVNPEGVDGNPDPLKTAHDVRVTFARMAMNDEETVALTAGGHTVGKCHGNGNAALLGPEPEGADVEDQGLGWINKTQSGIGRNAVTSGLEGAWTPHPTQWDNGYFRMLLNYDWELKKSPAGAWQWEPINPREEDLPVDVEDPSIRRNLVMTDADMAMKMDPEYRKISERFYQDPAYFADVFARAWFKLTHRDMGPKARYIGPDVPQEDLIWQDPIPAGNRNYDVQAVKDRIAASGLSISELVSTAWDSARTYRNSDKRGGANGARIRLAPQKDWEGNEPDRLAKVLAVLEGIAAATGASVADVIVLAGNVGVEQAARAAGVEIVLPFAPGRGDATAEQTDTESFAVLEPIHDGYRNWLKQDYAATPEELLLDRTQLLGLTAPEMTVLIGGLRVLGTNHGGTKHGVFTDREGVLTNDFFVNLTDMNYLWKPAGKNLYEICDRKTNQVKWTATRVDLVFGSNSILRAYSELYAQDDNKEKFVRDFVAAWTKVMNADRFDLD 720
               SCOP domains d3wnua1 A:11-429 automated matches                                                                                                                                                                                                                                                                                                                                                                                                 d3wnua2 A:430-720 automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhh.............hhhhhhh..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................................ee...ee.................hhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..ee....hhhhh..hhhhhhhhhh...........hhhhh......ee.........hhhhhhhhhh.eeeee.....eeeee...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhhhh.............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhh..eehhhhee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhh.............hhhhhhhh...eeeee.....eeeee.....eeeeehhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEROXIDASE_4  PDB: A:455-720 UniProt: 455-720                                                                                                                                                                                                                              PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wnu A  11 MHGGATTVNISTAEWWPKALNLDILSQHDRKTNPMGPDFNYQEEVKKLDVAALKQDLQALMTDSQDWWPADWGHYGGLMIRLTWHAAGTYRIADGRGGAGTGNQRFAPLNSWPDNTNLDKARRLLWPIKQKYGNKLSWADLIAYAGTIAYESMGLKTFGFAFGREDIWHPEKDIYWGPEKEWVPPSTNPNSRYTGDRELENPLAAVTMGLIYVNPEGVDGNPDPLKTAHDVRVTFARMAMNDEETVALTAGGHTVGKCHGNGNAALLGPEPEGADVEDQGLGWINKTQSGIGRNAVTSGLEGAWTPHPTQWDNGYFRMLLNYDWELKKSPAGAWQWEPINPREEDLPVDVEDPSIRRNLVMTDADMAMKMDPEYRKISERFYQDPAYFADVFARAWFKLTHRDMGPKARYIGPDVPQEDLIWQDPIPAGNRNYDVQAVKDRIAASGLSISELVSTAWDSARTYRNSDKRGGANGARIRLAPQKDWEGNEPDRLAKVLAVLEGIAAATGASVADVIVLAGNVGVEQAARAAGVEIVLPFAPGRGDATAEQTDTESFAVLEPIHDGYRNWLKQDYAATPEELLLDRTQLLGLTAPEMTVLIGGLRVLGTNHGGTKHGVFTDREGVLTNDFFVNLTDMNYLWKPAGKNLYEICDRKTNQVKWTATRVDLVFGSNSILRAYSELYAQDDNKEKFVRDFVAAWTKVMNADRFDLD 720
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720

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: All alpha proteins (14657)

Fold: Heme-dependent peroxidases (402)

Superfamily: Heme-dependent peroxidases (402)

Family: automated matches (40)

Protein domain: automated matches (40)

Synechococcus elongatus [TaxId: 1140] (1)

1a	d3wnua1	A:11-429
1b	d3wnua2	A:430-720

(no "CATH Domain" information available for 3WNU)

(no "Pfam Domain" information available for 3WNU)

Asymmetric Unit(hide GO term definitions)

Chain A (KATG_SYNE7 | Q31MN3)

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.

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	Cis Peptide Bonds
		Ala A:117 - Pro A:118	[ RasMol ]
		Ala A:490 - Pro A:491	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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(no "Related Entries Specified in the PDB File" available for 3WNU)

Description

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Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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