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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CONFORMATIONAL MOBILITY IN THE ACTIVE SITE OF A HEME PEROXIDASE

Authors :   S. K. Badyal, M. G. Joyce, K. H. Sharp, E. L. Raven, P. C. E. Moody

Date :   27 Mar 06 (Deposition) - 13 Jun 06 (Release) - 07 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : X

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

Reference :   S. K. Badyal, M. G. Joyce, K. H. Sharp, H. E. Seward, M. Mewies, J. Basran I. K. Macdonald, P. C. E. Moody, E. L. Raven
Conformational Mobility In The Active Site Of A Heme Peroxidase.
J. Biol. Chem. V. 281 24512 2006
PubMed-ID: 16762924 | Reference-DOI: 10.1074/JBC.M602602200

Molecule 1 - CYTOSOLIC ASCORBATE PEROXIDASE 1
	Chains	:	X
	EC Number	:	1.11.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ASCORBATE PEROXIDASE
	Mutation	:	YES
	Organism Common	:	SOYBEAN
	Organism Scientific	:	GLYCINE MAX
	Organism Taxid	:	3847

		1
Asymmetric/Biological Unit	:	X

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR X:164 , THR X:180 , ASN X:182 , ILE X:185 , ASP X:187	BINDING SITE FOR RESIDUE NA X 9252
2	AC2	SOFTWARE	PRO X:34 , PRO X:132 , ALA X:134 , PHE X:145 , LEU X:159 , SER X:160 , GLY X:162 , HIS X:163 , ILE X:165 , GLY X:166 , ALA X:167 , ALA X:168 , HIS X:169 , ARG X:172 , SER X:173 , TRP X:179 , LEU X:205 , SER X:207 , TYR X:235 , HOH X:9253 , HOH X:9257 , HOH X:9273 , HOH X:9275 , HOH X:9313	BINDING SITE FOR RESIDUE HEM X 251

(no "SS Bond" information available for 2GHE)

(no "Cis Peptide Bond" information available for 2GHE)

(no "SAP(SNP)/Variant" information available for 2GHE)

(no "PROSITE Motif" information available for 2GHE)

(no "Exon" information available for 2GHE)

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 X from PDB  Type:PROTEIN  Length:250
 aligned with Q43758_SOYBN | Q43758 from UniProtKB/TrEMBL  Length:250

    Alignment length:250
                                    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
         Q43758_SOYBN     1 MGKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA 250
               SCOP domains d2ghex_ X: Ascorbate peroxidase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2gheX01 X:1-131,X:239-250  [code=1.10.520.10, no name defined]                                                                     2gheX02 X:132-238 Peroxidase, domain 2                                                                     2gheX01      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh............................hhhhhhhhhh.....hhhhhhhhhhhhhh.ee........ee.........hhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ghe X   1 SGKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAAHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA 250
                                    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

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: Ascorbate peroxidase (11)

Soybean (Glycine max) [TaxId: 3847] (9)

d2ghex_

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)

Soybean (Glycine max) (22)

2gheX01

X:1-131,X:239-250

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Soybean (Glycine max) (22)

2gheX02

X:132-238

(no "Pfam Domain" information available for 2GHE)

Asymmetric/Biological Unit(hide GO term definitions)

Chain X (Q43758_SOYBN | Q43758)

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: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.

Asymmetric/Biological Unit
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		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ghe)

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	1.11.1.11
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (2, 2)

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Gene Ontology (8, 8)

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