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Asym./Biol. Unit (Jmol Viewer)

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Title :   HEME LIGAND MUTANT OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID

Authors :   K. Meno, C. G. White, A. T. Smith, M. Gajhede

Date :   16 Dec 98 (Deposition) - 28 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase, Peroxidase, Heme Enzyme, Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Meno, C. G. White, A. T. Smith, M. Gajhede
Structural And Catalytical Implications Of A F221M Mutation In The Proximal Pocket Of Horseradish Peroxidase C (Hrp C)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTEIN (HORSERADISH PEROXIDASE C1A)
	Chains	:	A, B
	EC Number	:	1.11.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	ARMORACIA RUSTICANA
	Organism Taxid	:	3704
	Other Details	:	CONTAINS HEME, TWO STRUCTURAL CALCIUM IONS, AND BENZHYDROXAMIC ACID BOUND IN ACTIVE SITE
	Synonym	:	HRP C, HRP C1A

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	BHO	2	Ligand/Ion	BENZHYDROXAMIC ACID
2	CA	4	Ligand/Ion	CALCIUM ION
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:171 , ASP A:222 , THR A:225 , ILE A:228 , ASP A:230	BINDING SITE FOR RESIDUE CA A 351
02	AC2	SOFTWARE	ASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:721	BINDING SITE FOR RESIDUE CA A 352
03	AC3	SOFTWARE	THR B:171 , ASP B:222 , THR B:225 , ILE B:228 , ASP B:230	BINDING SITE FOR RESIDUE CA B 351
04	AC4	SOFTWARE	ASP B:43 , VAL B:46 , GLY B:48 , ASP B:50 , SER B:52 , HOH B:1721	BINDING SITE FOR RESIDUE CA B 352
05	AC5	SOFTWARE	ARG A:31 , ALA A:34 , SER A:35 , ARG A:38 , PHE A:41 , SER A:73 , PRO A:139 , ALA A:140 , PRO A:141 , LEU A:166 , GLY A:169 , HIS A:170 , PHE A:172 , GLY A:173 , LYS A:174 , ASN A:175 , GLN A:176 , PHE A:179 , MET A:221 , ILE A:244 , SER A:246 , BHO A:353 , HOH A:711 , HOH A:768 , HOH A:802 , HOH A:803	BINDING SITE FOR RESIDUE HEM A 350
06	AC6	SOFTWARE	ARG A:38 , PHE A:41 , HIS A:42 , PHE A:68 , GLY A:69 , PRO A:139 , PRO A:141 , PHE A:179 , HEM A:350 , HOH A:711	BINDING SITE FOR RESIDUE BHO A 353
07	AC7	SOFTWARE	ARG B:31 , ALA B:34 , SER B:35 , ARG B:38 , PHE B:41 , SER B:73 , PRO B:139 , ALA B:140 , PRO B:141 , LEU B:166 , GLY B:169 , HIS B:170 , PHE B:172 , GLY B:173 , LYS B:174 , ASN B:175 , GLN B:176 , PHE B:179 , MET B:221 , ILE B:244 , SER B:246 , BHO B:354 , HOH B:1711 , HOH B:1768 , HOH B:1802 , HOH B:1803	BINDING SITE FOR RESIDUE HEM B 350
08	AC8	SOFTWARE	ARG B:38 , PHE B:41 , HIS B:42 , PHE B:68 , GLY B:69 , PRO B:139 , PRO B:141 , PHE B:179 , HEM B:350 , HOH B:1711	BINDING SITE FOR RESIDUE BHO B 354
09	BEM	AUTHOR	ARG B:38 , HIS B:42 , PHE B:68 , GLY B:69 , PRO B:139 , ALA B:140 , PRO B:141 , PHE B:179	BENZHYDROZAMIC ACID BINDING SITE.
10	BEN	AUTHOR	ARG A:38 , HIS A:42 , PHE A:68 , GLY A:69 , PRO A:139 , ALA A:140 , PRO A:141 , PHE A:179	BENZHYDROZAMIC ACID BINDING SITE.

Asymmetric/Biological Unit

No.	Residues
1	B:11	-	B:91
2	B:44	-	B:49
3	B:97	-	B:301
4	B:177	-	B:209

(no "Cis Peptide Bond" information available for 3ATJ)

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_4	PS50873	Plant heme peroxidase family profile.	PER1A_ARMRU	31-335	2	A:1-305 B:1-305
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	PER1A_ARMRU	63-74	2	A:33-44 B:33-44
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	PER1A_ARMRU	192-202	2	A:162-172 B:162-172

(no "Exon" information available for 3ATJ)

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:308
 aligned with PER1A_ARMRU | P00433 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:308
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329        
          PER1A_ARMRU    30 AQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSN 337
               SCOP domains d3atja_ A: Plant peroxidase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --3atjA01 A:2-138,A:285-305  [code=1.10.520.10, no name defined]                                                                           3atjA02 A:139-284 Peroxidase, domain 2                                                                                                            3atjA01              -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhh.........hhh..........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...................hhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhh..eeehhh.hhhhh.hhh.........hhhhhhhhhh.........eee..........hhhhhhhhh.....hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PEROXIDASE_4  PDB: A:1-305 UniProt: 31-335                                                                                                                                                                                                                                                                       -- PROSITE (1)
                PROSITE (2) ---------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3atj A   0 MQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDMDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSN 307
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299

Chain B from PDB  Type:PROTEIN  Length:308
 aligned with PER1A_ARMRU | P00433 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:308
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329        
          PER1A_ARMRU    30 AQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSN 337
               SCOP domains d3atjb_ B: Plant peroxidase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --3atjB01 B:2-138,B:285-305  [code=1.10.520.10, no name defined]                                                                           3atjB02 B:139-284 Peroxidase, domain 2                                                                                                            3atjB01              -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhh.........hhh..........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...................hhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhh..eeehhh.hhhhh.hhh.........hhhhhhhhhh.........eee..........hhhhhhhhh.....hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PEROXIDASE_4  PDB: B:1-305 UniProt: 31-335                                                                                                                                                                                                                                                                       -- PROSITE (1)
                PROSITE (2) ---------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3atj B   0 MQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDMDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSN 307
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Heme-dependent peroxidases (402)

Superfamily: Heme-dependent peroxidases (402)

Family: CCP-like (292)

Protein domain: Plant peroxidase (35)

Horseradish (Armoracia rusticana) [TaxId: 3704] (29)

1a	d3atja_	A:
1b	d3atjb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Peroxidase; domain 1 (244)

Homologous Superfamily: [code=1.10.520.10, no name defined] (241)

Armoracia rusticana. Organism_taxid: 3704. (6)

1a	3atjA01	A:2-138,A:285-305
1b	3atjB01	B:2-138,B:285-305

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Armoracia rusticana. Organism_taxid: 3704. (6)

2a	3atjA02	A:139-284
2b	3atjB02	B:139-284

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PER1A_ARMRU | P00433)

molecular function
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (10, 10)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

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