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Title :   CRYSTAL STRUCTURE OF RECOMBINANT ASCORBATE PEROXIDASE

Authors :   W. R. Patterson, T. L. Poulos

Date :   01 Feb 95 (Deposition) - 08 Mar 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

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

Reference :   W. R. Patterson, T. L. Poulos
Crystal Structure Of Recombinant Pea Cytosolic Ascorbate Peroxidase.
Biochemistry V. 34 4331 1995
PubMed-ID: 7703247 | Reference-DOI: 10.1021/BI00013A023
(for further references see the PDB file header)

Molecule 1 - CYTOSOLIC ASCORBATE PEROXIDASE
	Chains	:	A, B, C, D
	EC Number	:	1.11.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CDNA
	Organism Common	:	PEA
	Organism Scientific	:	PISUM SATIVUM
	Organism Taxid	:	3888

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	K	4	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:164 , THR A:180 , ASN A:182 , ILE A:185 , ASP A:187	BINDING SITE FOR RESIDUE K A 252
02	AC2	SOFTWARE	THR B:164 , THR B:180 , ASN B:182 , ILE B:185 , ASP B:187	BINDING SITE FOR RESIDUE K B 252
03	AC3	SOFTWARE	THR C:164 , THR C:180 , ASN C:182 , ILE C:185 , ASP C:187	BINDING SITE FOR RESIDUE K C 252
04	AC4	SOFTWARE	THR D:164 , THR D:180 , ASN D:182 , ILE D:185 , ASP D:187	BINDING SITE FOR RESIDUE K D 252
05	AC5	SOFTWARE	PRO A:34 , TRP A:41 , PRO A:132 , ALA A:134 , PHE A:145 , LEU A:159 , HIS A:163 , ILE A:165 , GLY A:166 , ALA A:167 , ALA A:168 , HIS A:169 , ARG A:172 , SER A:173 , TRP A:179 , TYR A:235 , HOH A:294 , HOH A:295 , HOH A:322 , HOH A:716	BINDING SITE FOR RESIDUE HEM A 251
06	AC6	SOFTWARE	PRO B:34 , TRP B:41 , PRO B:132 , ALA B:134 , LEU B:141 , PHE B:145 , LEU B:159 , HIS B:163 , ILE B:165 , GLY B:166 , ALA B:167 , ALA B:168 , HIS B:169 , ARG B:172 , SER B:173 , TRP B:179 , TYR B:235 , HOH B:266 , HOH B:280 , HOH B:364 , HOH B:855	BINDING SITE FOR RESIDUE HEM B 251
07	AC7	SOFTWARE	PRO C:34 , TRP C:41 , PRO C:132 , PHE C:145 , LEU C:159 , SER C:160 , HIS C:163 , ILE C:165 , GLY C:166 , ALA C:167 , HIS C:169 , ARG C:172 , SER C:173 , TRP C:179 , TYR C:235 , HOH C:268 , HOH C:272	BINDING SITE FOR RESIDUE HEM C 251
08	AC8	SOFTWARE	PRO D:34 , TRP D:41 , ALA D:134 , PHE D:145 , LEU D:159 , SER D:160 , GLY D:162 , HIS D:163 , ILE D:165 , GLY D:166 , ALA D:167 , ALA D:168 , HIS D:169 , ARG D:172 , SER D:173 , TRP D:179 , SER D:207 , TYR D:235 , HOH D:434 , HOH D:435 , HOH D:822	BINDING SITE FOR RESIDUE HEM D 251
09	K1	AUTHOR	K A:252 , THR A:164 , THR A:180 , ASN A:182 , ILE A:185 , ASP A:187	COORDINATING CARBONYL OXYGEN AND SIDE-CHAIN LIGANDS FOR POTASSIUM ION IN CHAIN A
10	K2	AUTHOR	K B:252 , THR B:164 , THR B:180 , ASN B:182 , ILE B:185 , ASP B:187	COORDINATING CARBONYL OXYGEN AND SIDE-CHAIN LIGANDS FOR POTASSIUM ION IN CHAIN B
11	K3	AUTHOR	K C:252 , THR C:164 , THR C:180 , ASN C:182 , ILE C:185 , ASP C:187	COORDINATING CARBONYL OXYGEN AND SIDE-CHAIN LIGANDS FOR POTASSIUM ION IN CHAIN C
12	K4	AUTHOR	K D:252 , THR D:164 , THR D:180 , ASN D:182 , ILE D:185 , ASP D:187	COORDINATING CARBONYL OXYGEN AND SIDE-CHAIN LIGANDS FOR POTASSIUM ION IN CHAIN D

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

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	APX1_PEA	33-44	4	A:33-44 B:33-44 C:33-44 D:33-44
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	APX1_PEA	155-165	4	A:155-165 B:155-165 C:155-165 D:155-165

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	APX1_PEA	33-44	2	A:33-44 B:33-44 - -
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	APX1_PEA	155-165	2	A:155-165 B:155-165 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	APX1_PEA	33-44	2	- - C:33-44 D:33-44
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	APX1_PEA	155-165	2	- - C:155-165 D:155-165

(no "Exon" information available for 1APX)

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:249
 aligned with APX1_PEA | P48534 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
             APX1_PEA     2 GKSYPTVSPDYQKAIEKAKRKLRGFIAEKKCAPLILRLAWHSAGTFDSKTKTGGPFGTIKHQAELAHGANNGLDIAVRLLEPIKEQFPIVSYADFYQLAGVVAVEITGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLSDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLTGEKDGLLQLPSDKALLTDSVFRPLVEKYAADEDVFFADYAEAHLKLSELGFAEA 250
               SCOP domains d1apxa_ A: Ascorbate peroxidase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1apxA01 A:2-131,A:239-250  [code=1.10.520.10, no name defined]                                                                    1apxA02 A:132-238 Peroxidase, domain 2                                                                     1apxA01      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..................hhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...............................hhhhhhhhhh...hhhhhhhh......eehhhhhh..ee..........hhhhhhhh.........hhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------PEROXIDASE_------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1apx A   2 GKSYPTVSPDYQKAIEKAKRKLRGFIAEKKCAPLILRLAWHSAGTFDSKTKTGGPFGTIKHQAELAHGANNGLDIAVRLLEPIKEQFPIVSYADFYQLAGVVAVEITGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLSDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLTGEKDGLLQLPSDKALLTDSVFRPLVEKYAADEDVFFADYAEAHLKLSELGFAEA 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with APX1_PEA | P48534 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
             APX1_PEA     2 GKSYPTVSPDYQKAIEKAKRKLRGFIAEKKCAPLILRLAWHSAGTFDSKTKTGGPFGTIKHQAELAHGANNGLDIAVRLLEPIKEQFPIVSYADFYQLAGVVAVEITGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLSDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLTGEKDGLLQLPSDKALLTDSVFRPLVEKYAADEDVFFADYAEAHLKLSELGFAEA 250
               SCOP domains d1apxb_ B: Ascorbate peroxidase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1apxB01 B:2-131,B:239-250  [code=1.10.520.10, no name defined]                                                                    1apxB02 B:132-238 Peroxidase, domain 2                                                                     1apxB01      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................................................................................................................................................................ee........ee........................................................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------PEROXIDASE_------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1apx B   2 GKSYPTVSPDYQKAIEKAKRKLRGFIAEKKCAPLILRLAWHSAGTFDSKTKTGGPFGTIKHQAELAHGANNGLDIAVRLLEPIKEQFPIVSYADFYQLAGVVAVEITGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLSDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLTGEKDGLLQLPSDKALLTDSVFRPLVEKYAADEDVFFADYAEAHLKLSELGFAEA 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain C from PDB  Type:PROTEIN  Length:249
 aligned with APX1_PEA | P48534 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
             APX1_PEA     2 GKSYPTVSPDYQKAIEKAKRKLRGFIAEKKCAPLILRLAWHSAGTFDSKTKTGGPFGTIKHQAELAHGANNGLDIAVRLLEPIKEQFPIVSYADFYQLAGVVAVEITGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLSDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLTGEKDGLLQLPSDKALLTDSVFRPLVEKYAADEDVFFADYAEAHLKLSELGFAEA 250
               SCOP domains d1apxc_ C: Ascorbate peroxidase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1apxC01 C:2-131,C:239-250  [code=1.10.520.10, no name defined]                                                                    1apxC02 C:132-238 Peroxidase, domain 2                                                                     1apxC01      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................................................................................................................................................................ee........ee........................................................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------PEROXIDASE_------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1apx C   2 GKSYPTVSPDYQKAIEKAKRKLRGFIAEKKCAPLILRLAWHSAGTFDSKTKTGGPFGTIKHQAELAHGANNGLDIAVRLLEPIKEQFPIVSYADFYQLAGVVAVEITGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLSDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLTGEKDGLLQLPSDKALLTDSVFRPLVEKYAADEDVFFADYAEAHLKLSELGFAEA 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain D from PDB  Type:PROTEIN  Length:249
 aligned with APX1_PEA | P48534 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
             APX1_PEA     2 GKSYPTVSPDYQKAIEKAKRKLRGFIAEKKCAPLILRLAWHSAGTFDSKTKTGGPFGTIKHQAELAHGANNGLDIAVRLLEPIKEQFPIVSYADFYQLAGVVAVEITGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLSDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLTGEKDGLLQLPSDKALLTDSVFRPLVEKYAADEDVFFADYAEAHLKLSELGFAEA 250
               SCOP domains d1apxd_ D: Ascorbate peroxidase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1apxD01 D:2-131,D:239-250  [code=1.10.520.10, no name defined]                                                                    1apxD02 D:132-238 Peroxidase, domain 2                                                                     1apxD01      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................................................................................................................................................................ee........ee........................................................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------PEROXIDASE_------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1apx D   2 GKSYPTVSPDYQKAIEKAKRKLRGFIAEKKCAPLILRLAWHSAGTFDSKTKTGGPFGTIKHQAELAHGANNGLDIAVRLLEPIKEQFPIVSYADFYQLAGVVAVEITGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLSDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLTGEKDGLLQLPSDKALLTDSVFRPLVEKYAADEDVFFADYAEAHLKLSELGFAEA 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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: CCP-like (292)

Protein domain: Ascorbate peroxidase (11)

Pea (Pisum sativum) [TaxId: 3888] (1)

1a	d1apxa_	A:
1b	d1apxb_	B:
1c	d1apxc_	C:
1d	d1apxd_	D:

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)

Pea (Pisum sativum) (1)

1a	1apxA01	A:2-131,A:239-250
1b	1apxB01	B:2-131,B:239-250
1c	1apxC01	C:2-131,C:239-250
1d	1apxD01	D:2-131,D:239-250

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Pea (Pisum sativum) (1)

2a	1apxA02	A:132-238
2b	1apxB02	B:132-238
2c	1apxC02	C:132-238
2d	1apxD02	D:132-238

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (APX1_PEA | P48534)

molecular function
	GO:0016688	L-ascorbate peroxidase activity	Catalysis of the reaction: L-ascorbate + hydrogen peroxide = dehydroascorbate + 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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1apx)

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	1apx
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	APX1_PEA \| P48534
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	APX1_PEA \| P48534
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	APX1_PEA \| P48534	:	3e2n

(no "Related Entries Specified in the PDB File" available for 1APX)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

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Related Entries Specified in the PDB File