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Title :   CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS

Authors :   K. Fukuyama, N. Kunishima, F. Amada

Date :   25 Apr 95 (Deposition) - 29 Jan 96 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Peroxidase (Donor:H2O2 Oxidoreductase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Fukuyama, N. Kunishima, F. Amada, T. Kubota, H. Matsubara
Crystal Structures Of Cyanide- And Triiodide-Bound Forms Of Arthromyces Ramosus Peroxidase At Different Ph Values. Perturbations Of Active Site Residues And Their Implication In Enzyme Catalysis.
J. Biol. Chem. V. 270 21884 1995
PubMed-ID: 7665612 | Reference-DOI: 10.1074/JBC.270.37.21884
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:111 , PHE A:114 , ASN A:143 , NAG A:349 , HOH A:700	BINDING SITE FOR RESIDUE NAG A 348
02	AC2	SOFTWARE	ALA A:82 , ARG A:104 , PHE A:114 , NAG A:348 , HOH A:963	BINDING SITE FOR RESIDUE NAG A 349
03	AC3	SOFTWARE	ASP A:57 , GLY A:75 , ASP A:77 , SER A:79 , HOH A:738 , HOH A:739	BINDING SITE FOR RESIDUE CA A 346
04	AC4	SOFTWARE	SER A:185 , ASP A:202 , THR A:204 , VAL A:207 , ASP A:209	BINDING SITE FOR RESIDUE CA A 347
05	AC5	SOFTWARE	HEM A:345 , IOD A:676 , IOD A:679 , HOH A:733	BINDING SITE FOR RESIDUE IOD A 675
06	AC6	SOFTWARE	ARG A:52 , HIS A:56 , HEM A:345 , IOD A:675 , IOD A:677	BINDING SITE FOR RESIDUE IOD A 676
07	AC7	SOFTWARE	ARG A:52 , HIS A:56 , HEM A:345 , IOD A:676	BINDING SITE FOR RESIDUE IOD A 677
08	AC8	SOFTWARE	GLY A:191 , IOD A:679	BINDING SITE FOR RESIDUE IOD A 678
09	AC9	SOFTWARE	IOD A:675 , IOD A:678 , IOD A:680	BINDING SITE FOR RESIDUE IOD A 679
10	BC1	SOFTWARE	IOD A:679 , IOD A:681	BINDING SITE FOR RESIDUE IOD A 680
11	BC2	SOFTWARE	IOD A:680 , HOH A:883	BINDING SITE FOR RESIDUE IOD A 681
12	BC3	SOFTWARE	HOH A:898	BINDING SITE FOR RESIDUE K A 682
13	BC4	SOFTWARE	ARG A:48 , LEU A:51 , ARG A:52 , PHE A:55 , GLY A:155 , LEU A:181 , ALA A:183 , HIS A:184 , LEU A:186 , ALA A:187 , SER A:188 , GLN A:189 , GLU A:190 , GLY A:191 , LEU A:192 , MET A:243 , SER A:245 , IOD A:675 , IOD A:676 , IOD A:677 , HOH A:690 , HOH A:691 , HOH A:714 , HOH A:733	BINDING SITE FOR RESIDUE HEM A 345
14	CA1	UNKNOWN	CA A:346 , ASP A:57 , GLY A:75 , ASP A:77 , SER A:79 , HOH A:738 , HOH A:739	NULL
15	CA2	UNKNOWN	CA A:347 , SER A:185 , ASP A:202 , THR A:204 , VAL A:207 , ASP A:209	NULL
16	GL1	UNKNOWN	NAG A:348 , NAG A:349 , ASN A:143	NULL

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:336
 aligned with PER_ARTRA | P28313 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:336
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358      
            PER_ARTRA    29 SVTCPGGQSTSNSQCCVWFDVLDDLQTNFYQGSKCESPVRKILRIVFHDAIGFSPALTAAGQFGGGGADGSIIAHSNIELAFPANGGLTDTIEALRAVGINHGVSFGDLIQFATAVGMSNCPGSPRLEFLTGRSNSSQPSPPSLIPGPGNTVTAILDRMGDAGFSPDEVVDLLAAHSLASQEGLNSAIFRSPLDSTPQVFDTQFYIETLLKGTTQPGPSLGFAEELSPFPGEFRMRSDALLARDSRTACRWQSMTSSNEVMGQRYRAAMAKMSVLGFDRNALTDCSDVIPSAVSNNAAPVIPGGLTVDDIEVSCPSEPFPEIATASGPLPSLAPAP 364
               SCOP domains d1arxa_ A: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -----------1arxA01 A:20-153,A:277-304  [code=1.10.520.10, no name defined]                                                                       1arxA02 A:154-276,A:305-344 Peroxidase, domain 2                                                                           1arxA01 A:20-153,A:277-304  1arxA02 A:154-276,A:305-344              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ................hhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhh..............hhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.........ee..........hhhhhh...............ee........-hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhh.........ee...............ee.....................ee............ Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ee----------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------------PEROXIDASE_-------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------PEROXIDASE_4  PDB: A:50-297 UniProt: 70-317                                                                                                                                                                                                             ----------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1arx A   9 SVTCPGGQSTSNSQCCVWFDVLDDLQTNFYQGSKCESPVRKILRIVFHDAIGFSPALTAAGQFGGGGADGSIIAHSNIELAFPANGGLTDTIEALRAVGINHGVSFGDLIQFATAVGMSNCPGSPRLEFLTGRSNSSQPSPPSLIPGPGNTVTAILDRMGDAGFSPDEVVDLLAAHSLASQEGLNSAIFRSPLDSTPQVFDTQFYIETLLKGTTQPGPSLGFAEELSPFPGEFRMRSDALLARDSRTACRWQSMTSSNEVMGQRYRAAMAKMSVLGFDRNALTDCSDVIPSAVSNNAAPVIPGGLTVDDIEVSCPSEPFPEIATASGPLPSLAPAP 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PER_ARTRA | P28313)

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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