1GX2 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   RECOMBINANT HORSERADISH PEROXIDASE PHE209SER COMPLEX WITH BENZHYDROXAMIC ACID

Authors :   K. Meno, M. Gajhede, A. Henriksen

Date :   26 Mar 02 (Deposition) - 28 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

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

Reference :   A. Henriksen, N. Brissett, K. Meno, O. Mirza, M. Gajhede
Hrpc Heme Crevice Architecture
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PEROXIDASE C1A
	Chains	:	A, B
	EC Number	:	1.11.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	HORSERADISH
	Organism Scientific	:	ARMORACIA RUSTICANA
	Organism Taxid	:	3704
	Other Details	:	SYNTHETIC GENE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric 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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:171 , ASP A:222 , THR A:225 , ILE A:228 , ASP A:230	BINDING SITE FOR RESIDUE CA A1310
2	AC2	SOFTWARE	ASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:2040	BINDING SITE FOR RESIDUE CA A1311
3	AC3	SOFTWARE	THR B:171 , ASP B:222 , THR B:225 , ILE B:228 , ASP B:230	BINDING SITE FOR RESIDUE CA B1310
4	AC4	SOFTWARE	ASP B:43 , VAL B:46 , GLY B:48 , ASP B:50 , SER B:52 , HOH B:2040	BINDING SITE FOR RESIDUE CA B1311
5	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:221 , SER A:246 , BHO A:1309 , HOH A:2024 , HOH A:2182 , HOH A:2183 , HOH A:2184 , HOH A:2185	BINDING SITE FOR RESIDUE HEM A1308
6	AC6	SOFTWARE	ARG A:38 , PHE A:41 , HIS A:42 , PHE A:68 , PRO A:139 , HEM A:1308 , HOH A:2185	BINDING SITE FOR RESIDUE BHO A1309
7	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:221 , SER B:246 , BHO B:1309 , HOH B:2027 , HOH B:2184 , HOH B:2185 , HOH B:2186 , HOH B:2187	BINDING SITE FOR RESIDUE HEM B1308
8	AC8	SOFTWARE	ARG B:38 , PHE B:41 , HIS B:42 , PHE B:68 , PRO B:139 , HEM B:1308 , HOH B:2187	BINDING SITE FOR RESIDUE BHO B1309

Asymmetric Unit

No.	Residues
1	A:11	-	A:91
2	A:11	-	A:91
3	A:44	-	A:49
4	A:97	-	A:301
5	A:177	-	A:209
6	B:11	-	B:91
7	B:11	-	B:91
8	B:44	-	B:49
9	B:97	-	B:301
10	B:177	-	B:209

(no "Cis Peptide Bond" information available for 1GX2)

(no "SAP(SNP)/Variant" information available for 1GX2)

Asymmetric 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

Biological Unit 1 (3, 3)

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

Biological Unit 2 (3, 3)

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

(no "Exon" information available for 1GX2)

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:309
 aligned with PER1A_ARMRU | P00433 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:309
                                    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 AQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSNS 338
               SCOP domains d1gx2a_ A: Plant peroxidase                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --1gx2A01 A:2-138,A:285-305  [code=1.10.520.10, no name defined]                                                                           1gx2A02 A:139-284 Peroxidase, domain 2                                                                                                            1gx2A01              --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhh.......hhhhh........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.................hhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.eee...hhhhhhhhhhh.......hhhhhhhhhhhh........eee..........hhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................... 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
                 1gx2 A   0 MQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRSIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSNS 308
                                     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:309
 aligned with PER1A_ARMRU | P00433 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:309
                                    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 AQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSNS 338
               SCOP domains d1gx2b_ B: Plant peroxidase                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --1gx2B01 B:2-138,B:285-305  [code=1.10.520.10, no name defined]                                                                           1gx2B02 B:139-284 Peroxidase, domain 2                                                                                                            1gx2B01              --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhh.......hhhhh........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.................hhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.eee...hhhhhhhhhhh.......hhhhhhhhhhhh........eee..........hhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................... 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
                 1gx2 B   0 MQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRSIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSNS 308
                                     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 Unit

Classes(

)

Folds(

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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	d1gx2a_	A:
1b	d1gx2b_	B:

Asymmetric 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)

Horseradish (Armoracia rusticana) (23)

1a	1gx2A01	A:2-138,A:285-305
1b	1gx2B01	B:2-138,B:285-305

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Horseradish (Armoracia rusticana) (23)

2a	1gx2A02	A:139-284
2b	1gx2B02	B:139-284

(no "Pfam Domain" information available for 1GX2)

Asymmetric 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.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1gx2)

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	1gx2
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	1.11.1.7
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1atj	RECOMBINANT HORSERADISH PEROXIDASE C1A
1gw2	RECOMBINANT HORSERADISH PEROXIDASE C1A THR171SER IN COMPLEX WITH FERULIC ACID
1gwo	RECOMBINANT HORSERADISH PEROXIDASE C1A ALA140GLN
1gwt	RECOMBINANT HORSERADISH PEROXIDASE C1A PHE221MET
1gwu	RECOMBINANT HORSERADISH PEROXIDASE C1A ALA140GLY
1h55	STRUCTURE OF HORSERADISH PEROXIDASE C1A COMPOUND II
1h57	STRUCTURE OF HORSERADISH PEROXIDASE C1A COMPOUND III
1h58	STRUCTURE OF FERROUS HORSERADISH PEROXIDASE C1A
1h5a	STRUCTURE OF FERRIC HORSERADISH PEROXIDASE C1A IN COMPLEX WITH ACETATE
1h5c	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (100-200% DOSE)
1h5d	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (0-11% DOSE)
1h5e	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (11-22% DOSE)
1h5f	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (22-33% DOSE)
1h5g	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (33-44% DOSE)
1h5h	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (44-56% DOSE)
1h5i	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (56-67% DOSE)
1h5j	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (67-78% DOSE)
1h5k	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (78-89% DOSE)
1h5l	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (89-100% DOSE)
1h5m	X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (0-100% DOSE)
1hch	HORSERADISH PEROXIDASE COMPOUND I
1kzm	DISTAL HEME POCKET MUTANT (R38S/H42E) OF RECOMBINANTHORSERADISH PEROXIDASE C (HRP C).
2atj	RECOMBINANT HORSERADISH PEROXIDASE COMPLEX WITH BENZHYDROXAMIC ACID
3atj	HEME LIGAND MUTANT OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID
4atj	DISTAL HEME POCKET MUTANT (H42E) OF RECOMBINANT HORSERADISHPEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID
6atj	RECOMBINANT HORSERADISH PEROXIDASE C COMPLEX WITH FERULIC ACID
7atj	RECOMBINANT HORSERADISH PEROXIDASE C1A COMPLEX WITH CYANIDE AND FERULIC ACID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (10, 10)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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