3VED - JenaLib

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Title :   RHODOCOCCUS JOSTII RHA1 DYPB D153H VARIANT IN COMPLEX WITH HEME

Authors :   J. C. Grigg, R. Singh, Z. Armstrong, L. D. Eltis, M. E. P. Murphy

Date :   07 Jan 12 (Deposition) - 18 Jan 12 (Release) - 29 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

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

Reference :   R. Singh, J. C. Grigg, Z. Armstrong, M. E. Murphy, L. D. Eltis
Distal Heme Pocket Residues Of B-Type Dye-Decolorizing Peroxidase: Arginine But Not Aspartate Is Essential For Peroxidase Activity.
J. Biol. Chem. V. 287 10623 2012
PubMed-ID: 22308037 | Reference-DOI: 10.1074/JBC.M111.332171

Molecule 1 - DYPB
	Chains	:	A, B, C
	EC Number	:	1.11.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	DYPB, RHA1_RO02407
	Mutation	:	YES
	Organism Scientific	:	RHODOCOCCUS JOSTII
	Organism Taxid	:	101510
	Strain	:	RHA1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	HEM	6	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:147 , PHE A:151 , VAL A:152 , HIS A:153 , GLY A:154 , THR A:155 , GLU A:156 , GLN A:185 , TYR A:187 , HIS A:189 , ILE A:206 , ARG A:208 , HIS A:226 , VAL A:227 , ASN A:230 , ARG A:244 , PHE A:261 , MET A:274 , LEU A:275 , MET A:278 , SER A:294 , CL A:404 , HOH A:527 , HOH A:533 , HOH A:535 , HOH A:552	BINDING SITE FOR RESIDUE HEM A 401
02	AC2	SOFTWARE	LYS A:113 , PHE A:117 , HIS A:138	BINDING SITE FOR RESIDUE CL A 402
03	AC3	SOFTWARE	ALA A:111 , ARG A:112 , LYS A:113 , HOH A:530 , HOH A:537 , HOH A:597 , HOH A:620 , ARG B:112 , LYS B:113	BINDING SITE FOR RESIDUE GOL A 403
04	AC4	SOFTWARE	HIS A:153 , ARG A:244 , ASN A:246 , HEM A:401	BINDING SITE FOR RESIDUE CL A 404
05	AC5	SOFTWARE	VAL B:152 , HIS B:153 , GLY B:154 , THR B:155 , GLU B:156 , GLN B:185 , TYR B:187 , HIS B:189 , ARG B:208 , HIS B:226 , VAL B:227 , ASN B:230 , ARG B:244 , PHE B:261 , LEU B:275 , MET B:278 , SER B:294 , CL B:403 , HOH B:571 , HOH B:572 , HOH B:580	BINDING SITE FOR RESIDUE HEM B 401
06	AC6	SOFTWARE	LYS B:113 , HIS B:138	BINDING SITE FOR RESIDUE CL B 402
07	AC7	SOFTWARE	HIS B:153 , ARG B:244 , ASN B:246 , HEM B:401	BINDING SITE FOR RESIDUE CL B 403
08	AC8	SOFTWARE	ASP C:147 , PHE C:151 , VAL C:152 , HIS C:153 , GLY C:154 , THR C:155 , GLU C:156 , GLN C:185 , TYR C:187 , HIS C:189 , ARG C:208 , HIS C:226 , VAL C:227 , ASN C:230 , ARG C:244 , PHE C:261 , MET C:274 , LEU C:275 , MET C:278 , VAL C:290 , SER C:294 , CL C:403 , HOH C:528 , HOH C:543	BINDING SITE FOR RESIDUE HEM C 401
09	AC9	SOFTWARE	LYS C:113 , PHE C:117 , HIS C:138	BINDING SITE FOR RESIDUE CL C 402
10	BC1	SOFTWARE	HIS C:153 , ARG C:244 , ASN C:246 , HEM C:401	BINDING SITE FOR RESIDUE CL C 403

(no "SS Bond" information available for 3VED)

Asymmetric Unit

No.	Residues
1	Glu A:282	-	Pro A:283
2	Glu B:282	-	Pro B:283
3	Glu C:282	-	Pro C:283

(no "SAP(SNP)/Variant" information available for 3VED)

(no "PROSITE Motif" information available for 3VED)

(no "Exon" information available for 3VED)

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:308
 aligned with Q0SE24_RHOJR | Q0SE24 from UniProtKB/TrEMBL  Length:350

    Alignment length:308
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305        
         Q0SE24_RHOJR     6 ARLAPQAVLTPPSAASLFLVLVAGDSDDDRATVCDVISGIDGPLKAVGFRELAGSLSCVVGVGAQFWDRVSASSKPAHLHPFVPLSGPVHSAPSTPGDLLFHIKAARKDLCFELGRQIVSALGSAATVVDEVHGFRYFDSRDLLGFVDGTENPTDDDAADSALIGDEDPDFRGGSYVIVQKYLHDMSAWNTLSTEEQERVIGRTKLENVELDDDAQPSNSHVTLNTIVDDDGVEHDILRDNMAFGSLGEAEYGTYFIGYAKDPAVTELMLRRMFLGEPPGNYDRVLDFSTAATGTLFFVPSRDVLESL 313
               SCOP domains d3veda_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhh.............ee....ee......eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..................hhhhhhhhhh....hhhhh..eeeeeeeeeehhhhhhhhhhhhhhhhhh.................hhhhhh.ee.....ee..ee..eeeee....eeeeeeeeee.hhhhhhhhhhhhhh.......hhhhh.eee...eeeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ved A   6 ARLAPQAVLTPPSAASLFLVLVAGDSDDDRATVCDVISGIDGPLKAVGFRELAGSLSCVVGVGAQFWDRVSASSKPAHLHPFVPLSGPVHSAPSTPGDLLFHIKAARKDLCFELGRQIVSALGSAATVVDEVHGFRYFDSRDLLGFVHGTENPTDDDAADSALIGDEDPDFRGGSYVIVQKYLHDMSAWNTLSTEEQERVIGRTKLENVELDDDAQPSNSHVTLNTIVDDDGVEHDILRDNMAFGSLGEAEYGTYFIGYAKDPAVTELMLRRMFLGEPPGNYDRVLDFSTAATGTLFFVPSRDVLESL 313
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with Q0SE24_RHOJR | Q0SE24 from UniProtKB/TrEMBL  Length:350

    Alignment length:309
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305         
         Q0SE24_RHOJR     6 ARLAPQAVLTPPSAASLFLVLVAGDSDDDRATVCDVISGIDGPLKAVGFRELAGSLSCVVGVGAQFWDRVSASSKPAHLHPFVPLSGPVHSAPSTPGDLLFHIKAARKDLCFELGRQIVSALGSAATVVDEVHGFRYFDSRDLLGFVDGTENPTDDDAADSALIGDEDPDFRGGSYVIVQKYLHDMSAWNTLSTEEQERVIGRTKLENVELDDDAQPSNSHVTLNTIVDDDGVEHDILRDNMAFGSLGEAEYGTYFIGYAKDPAVTELMLRRMFLGEPPGNYDRVLDFSTAATGTLFFVPSRDVLESLG 314
               SCOP domains d3vedb_ B: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhh.............ee....ee......eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..................hhhhhhhhhh....hhhhh..eeeeeeeeeehhhhhhh.hhhhhhhhhh.........hhhhh...hhhhhh............ee..eeeee....eeeeeeeeee.hhhhhhhhhhhhhhh......hhhhh.eee...eeeee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ved B   6 ARLAPQAVLTPPSAASLFLVLVAGDSDDDRATVCDVISGIDGPLKAVGFRELAGSLSCVVGVGAQFWDRVSASSKPAHLHPFVPLSGPVHSAPSTPGDLLFHIKAARKDLCFELGRQIVSALGSAATVVDEVHGFRYFDSRDLLGFVHGTENPTDDDAADSALIGDEDPDFRGGSYVIVQKYLHDMSAWNTLSTEEQERVIGRTKLENVELDDDAQPSNSHVTLNTIVDDDGVEHDILRDNMAFGSLGEAEYGTYFIGYAKDPAVTELMLRRMFLGEPPGNYDRVLDFSTAATGTLFFVPSRDVLESLG 314
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305

Chain C from PDB  Type:PROTEIN  Length:309
 aligned with Q0SE24_RHOJR | Q0SE24 from UniProtKB/TrEMBL  Length:350

    Alignment length:309
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305         
         Q0SE24_RHOJR     6 ARLAPQAVLTPPSAASLFLVLVAGDSDDDRATVCDVISGIDGPLKAVGFRELAGSLSCVVGVGAQFWDRVSASSKPAHLHPFVPLSGPVHSAPSTPGDLLFHIKAARKDLCFELGRQIVSALGSAATVVDEVHGFRYFDSRDLLGFVDGTENPTDDDAADSALIGDEDPDFRGGSYVIVQKYLHDMSAWNTLSTEEQERVIGRTKLENVELDDDAQPSNSHVTLNTIVDDDGVEHDILRDNMAFGSLGEAEYGTYFIGYAKDPAVTELMLRRMFLGEPPGNYDRVLDFSTAATGTLFFVPSRDVLESLG 314
               SCOP domains d3vedc_ C: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhh.............ee....ee......eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee...................hhhhhhhhh....hhhhh..eeeeeeeeeehhhhhhhhhhhhhhhhhh.................hhhhhh............ee..eeeee....eeeeeeeeee.hhhhhhhhhhhhhh.......hhhhh.eee...eeeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ved C   6 ARLAPQAVLTPPSAASLFLVLVAGDSDDDRATVCDVISGIDGPLKAVGFRELAGSLSCVVGVGAQFWDRVSASSKPAHLHPFVPLSGPVHSAPSTPGDLLFHIKAARKDLCFELGRQIVSALGSAATVVDEVHGFRYFDSRDLLGFVHGTENPTDDDAADSALIGDEDPDFRGGSYVIVQKYLHDMSAWNTLSTEEQERVIGRTKLENVELDDDAQPSNSHVTLNTIVDDDGVEHDILRDNMAFGSLGEAEYGTYFIGYAKDPAVTELMLRRMFLGEPPGNYDRVLDFSTAATGTLFFVPSRDVLESLG 314
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305

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: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Dimeric alpha+beta barrel (122)

Family: automated matches (41)

Protein domain: automated matches (41)

Rhodococcus jostii [TaxId: 101510] (8)

1a	d3veda_	A:
1b	d3vedb_	B:
1c	d3vedc_	C:

(no "CATH Domain" information available for 3VED)

(no "Pfam Domain" information available for 3VED)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q0SE24_RHOJR | Q0SE24)

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: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.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:282 - Pro A:283	[ RasMol ]
		Glu B:282 - Pro B:283	[ RasMol ]
		Glu C:282 - Pro C:283	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	3ved
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		Orientation in Membranes	:	OPM
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Access by UniProt ID/Accession number
	Q0SE24_RHOJR \| Q0SE24
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	1.11.1.-
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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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UniProtKB/TrEMBL
	Q0SE24_RHOJR \| Q0SE24	:	3qnr 3qns 3vec 3vee 3vef 3veg 4hov

3vec	RHODOCOCCUS JOSTII RHA1 DYPB D153A VARIANT IN COMPLEX WITH HEME
3vee	RHODOCOCCUS JOSTII RHA1 DYPB N246A VARIANT IN COMPLEX WITH HEME
3vef	RHODOCOCCUS JOSTII RHA1 DYPB N246H VARIANT IN COMPLEX WITH HEME
3veg	RHODOCOCCUS JOSTII RHA1 DYPB R244L VARIANT IN COMPLEX WITH HEME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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