1SCH - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PEANUT PEROXIDASE

Authors :   D. J. Schuller, T. L. Poulos

Date :   23 Jan 96 (Deposition) - 11 Jul 96 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.56

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

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

Reference :   D. J. Schuller, N. Ban, R. B. Huystee, A. Mcpherson, T. L. Poulos
The Crystal Structure Of Peanut Peroxidase.
Structure V. 4 311 1996
PubMed-ID: 8805539 | Reference-DOI: 10.1016/S0969-2126(96)00035-4

Molecule 1 - PEANUT PEROXIDASE, MAJOR CATIONIC ISOZYME
	Cellular Location	:	SECRETED, EXTRACELLULAR
	Chains	:	A, B
	EC Number	:	1.11.1.7
	Organism Common	:	PEANUT
	Organism Scientific	:	ARACHIS HYPOGAEA
	Organism Taxid	:	3818
	Other Details	:	CARBOHYDRATE PRESENT. ONE N-ACETYL GLUCOSAMINE SUGAR RESIDUE MODELED AT ASN 144 OF CHAIN B.
	Other Details - Source	:	CULTURED PEANUT CELLS
	Synonym	:	PNP

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN B:144	BINDING SITE FOR RESIDUE NAG B 303
02	AC2	SOFTWARE	THR A:170 , ASP A:214 , THR A:217 , LYS A:220 , ASP A:222	BINDING SITE FOR RESIDUE CA A 301
03	AC3	SOFTWARE	ASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:428	BINDING SITE FOR RESIDUE CA A 302
04	AC4	SOFTWARE	THR B:170 , ASP B:214 , THR B:217 , LYS B:220 , ASP B:222	BINDING SITE FOR RESIDUE CA B 301
05	AC5	SOFTWARE	ASP B:43 , VAL B:46 , GLY B:48 , ASP B:50 , SER B:52 , HOH B:458	BINDING SITE FOR RESIDUE CA B 302
06	AC6	SOFTWARE	ARG A:31 , ALA A:34 , SER A:35 , ARG A:38 , PHE A:41 , SER A:73 , ALA A:140 , LEU A:148 , PHE A:152 , LEU A:165 , ALA A:168 , HIS A:169 , GLY A:172 , GLN A:173 , ALA A:174 , GLN A:175 , ALA A:178 , PHE A:213 , SER A:238 , MET A:270 , HOH A:451 , HOH A:456	BINDING SITE FOR RESIDUE HEM A 300
07	AC7	SOFTWARE	ARG B:31 , ALA B:34 , SER B:35 , ARG B:38 , PHE B:41 , SER B:73 , ALA B:140 , PRO B:141 , LEU B:165 , SER B:166 , ALA B:168 , HIS B:169 , GLY B:172 , GLN B:173 , GLN B:175 , PHE B:213 , SER B:238 , HOH B:418	BINDING SITE FOR RESIDUE HEM B 300
08	ADC	UNKNOWN	ASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , GLU A:64	DISTAL CATION SITE THROUGH SOLVENT.
09	ADH	UNKNOWN	HIS A:42 , ARG A:38 , PHE A:41 , ASN A:70	DISTAL HEME POCKET.
10	APC	UNKNOWN	THR A:170 , ASP A:214 , THR A:217 , LYS A:220 , ASP A:222	PROXIMAL CATION SITE.
11	APH	UNKNOWN	HIS A:169 , PHE A:213 , ASP A:239	PROXIMAL HEME POCKET.
12	BDC	UNKNOWN	ASP B:43 , VAL B:46 , GLY B:48 , ASP B:50 , SER B:52 , GLU B:64	DISTAL CATION SITE THROUGH SOLVENT.
13	BDH	UNKNOWN	HIS B:42 , ARG B:38 , PHE B:41 , ASN B:70	DISTAL HEME POCKET.
14	BPC	UNKNOWN	THR B:170 , ASP B:214 , THR B:217 , LYS B:220 , ASP B:222	PROXIMAL CATION SITE.
15	BPH	UNKNOWN	HIS B:169 , PHE B:213 , ASP B:239	PROXIMAL HEME POCKET.

Asymmetric Unit

No.	Residues
1	A:11	-	A:91
2	A:44	-	A:49
3	A:97	-	A:290
4	A:176	-	A:201
5	B:11	-	B:91
6	B:44	-	B:49
7	B:97	-	B:290
8	B:176	-	B:201

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

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_4	PS50873	Plant heme peroxidase family profile.	PER1_ARAHY	23-316	2	A:2-294 B:2-294
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	PER1_ARAHY	55-66	2	A:33-44 B:33-44
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	PER1_ARAHY	183-193	2	A:161-171 B:161-171

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.	PER1_ARAHY	23-316	1	- B:2-294
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	PER1_ARAHY	55-66	1	- B:33-44
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	PER1_ARAHY	183-193	1	- B:161-171

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.	PER1_ARAHY	23-316	1	A:2-294 -
2	PEROXIDASE_2	PS00436	Peroxidases active site signature.	PER1_ARAHY	55-66	1	A:33-44 -
3	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	PER1_ARAHY	183-193	1	A:161-171 -

(no "Exon" information available for 1SCH)

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:294
 aligned with PER1_ARAHY | P22195 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:294
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312    
           PER1_ARAHY    23 QLSSNFYATKCPNALSTIKSAVNSAVAKEARMGASLLRLHFHDCFVQGCDASVLLDDTSNFTGEKTAGPNANSIRGFEVIDTIKSQVESLCPGVVSCADILAVAARDSVVALGGASWNVLLGRRDSTTASLSSANSDLPAPFFNLSGLISAFSNKGFTTKELVTLSGAHTIGQAQCTAFRTRIYNESNIDPTYAKSLQANCPSVGGDTNLSPFDVTTPNKFDNAYYINLRNKKGLLHSDQQLFNGVSTDSQVTAYSNNAATFNTDFGNAMIKMGNLSPLTGTSGQIRTNCRKTN 316
               SCOP domains d1scha_ A: Plant peroxidase                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -1schA01 A:2-138,A:274-294  [code=1.10.520.10, no name defined]                                                                           1schA02 A:139-273 Peroxidase, domain 2                                                                                                 1schA01               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...............................hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..................hhhhhhh........hhhhhhhhh....hhhhhhhh......eee...hhhhhhh......hhhhhhhhh.........eee...........hhhhhhh......hhhhh.......hhhhhhhhh.hhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PEROXIDASE_4  PDB: A:2-294 UniProt: 23-316                                                                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) --------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sch A   1 xLSSNFYATKCPNALSTIKSAVNSAVAKEARMGASLLRLHFHDCFVQGCDASVLLDDTSNFTGEKTAGPNANSIRGFEVIDTIKSQVESLCPGVVSCADILAVAARDSVVALGGASWNVLLGRRDSTTASLSSANSDLPAPFFNLSGLISAFSNKGFTTKELVTLSGAHTIGQAQCTAFRTRIYNESNIDPTYAKSLQANCPSVGGDTNLSPFDVTTPNKFDNAYYINLRNKKGLLHSDQQLFNGVSTDSQVTAYSNNAATFNTDFGNAMIKMGNLSPLTGTSGQIRTNCRKTN 294
                            |       10        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    
                            |                                                                                                                                                                                                                                                                                                     
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:294
 aligned with PER1_ARAHY | P22195 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:294
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312    
           PER1_ARAHY    23 QLSSNFYATKCPNALSTIKSAVNSAVAKEARMGASLLRLHFHDCFVQGCDASVLLDDTSNFTGEKTAGPNANSIRGFEVIDTIKSQVESLCPGVVSCADILAVAARDSVVALGGASWNVLLGRRDSTTASLSSANSDLPAPFFNLSGLISAFSNKGFTTKELVTLSGAHTIGQAQCTAFRTRIYNESNIDPTYAKSLQANCPSVGGDTNLSPFDVTTPNKFDNAYYINLRNKKGLLHSDQQLFNGVSTDSQVTAYSNNAATFNTDFGNAMIKMGNLSPLTGTSGQIRTNCRKTN 316
               SCOP domains d1schb_ B: Plant peroxidase                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -1schB01 B:2-138,B:274-294  [code=1.10.520.10, no name defined]                                                                           1schB02 B:139-273 Peroxidase, domain 2                                                                                                 1schB01               CATH domains
           Pfam domains (1) -----------------peroxidase-1schB01 B:18-258                                                                                                                                                                                                                      ------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------peroxidase-1schB02 B:18-258                                                                                                                                                                                                                      ------------------------------------ Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...............................hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..................hhhhhhh........hhhhhhhhh....hhhhhhhh......eee...hhhhhhh......hhhhhhhhh.........eee...........hhhhhhh......hhhhh.......hhhhhhhhh.hhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PEROXIDASE_4  PDB: B:2-294 UniProt: 23-316                                                                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) --------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sch B   1 xLSSNFYATKCPNALSTIKSAVNSAVAKEARMGASLLRLHFHDCFVQGCDASVLLDDTSNFTGEKTAGPNANSIRGFEVIDTIKSQVESLCPGVVSCADILAVAARDSVVALGGASWNVLLGRRDSTTASLSSANSDLPAPFFNLSGLISAFSNKGFTTKELVTLSGAHTIGQAQCTAFRTRIYNESNIDPTYAKSLQANCPSVGGDTNLSPFDVTTPNKFDNAYYINLRNKKGLLHSDQQLFNGVSTDSQVTAYSNNAATFNTDFGNAMIKMGNLSPLTGTSGQIRTNCRKTN 294
                            |       10        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    
                            1-PCA

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: Plant peroxidase (35)

Peanut (Arachis hypogaea) [TaxId: 3818] (1)

1a	d1scha_	A:
1b	d1schb_	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)

Peanut (Arachis hypogaea) (1)

1a	1schA01	A:2-138,A:274-294
1b	1schB01	B:2-138,B:274-294

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Peanut (Arachis hypogaea) (1)

2a	1schA02	A:139-273
2b	1schB02	B:139-273

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: peroxidase] (92)

Family: peroxidase (92)

Arachis hypogaea (Peanut) (1)

1a	peroxidase-1schB01	B:18-258
1b	peroxidase-1schB02	B:18-258

Asymmetric Unit(hide GO term definitions)

Chain A,B (PER1_ARAHY | P22195)

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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (15, 15)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

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