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Asym./Biol. Unit (Jmol Viewer)

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

Title :   SUPEROXIDE REDUCTASE (NEELAREDOXIN) FROM ARCHAEOGLOBUS FULGIDUS E12Q MUTANT

Authors :   T. M. Bandeiras, J. V. Rodrigues, C. M. Sousa, A. R. Barradas, F. G. Pinho A. F. Pinto, M. Teixeira, P. M. Matias, C. V. Romao

Date :   19 Mar 13 (Deposition) - 26 Mar 14 (Release) - 26 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Oxidoreductase, Oxygen Detoxification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. M. Bandeiras, J. V. Rodrigues, C. M. Sousa, A. R. Barradas, F. G. Pinho, A. F. Pinto, M. Teixeira, P. M. Matias, C. V. Romao
Understanding The Role Of Key Residues In The Superoxide Reductase Molecular Mechanism, Exploring Archaeoglobus Fulgidus Sor Structure
To Be Published
PubMed: search

Molecule 1 - SUPEROXIDE REDUCTASE
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7/NAFE12QA
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	SOR

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	FE	4	Ligand/Ion	FE (III) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:14 , HIS A:40 , HIS A:46 , CYS A:110 , HIS A:113 , HOH A:2007	BINDING SITE FOR RESIDUE FE A 201
2	AC2	SOFTWARE	HIS B:14 , HIS B:40 , HIS B:46 , CYS B:110 , HIS B:113 , HOH B:2006	BINDING SITE FOR RESIDUE FE B 201
3	AC3	SOFTWARE	HIS C:14 , HIS C:40 , HIS C:46 , CYS C:110 , HIS C:113	BINDING SITE FOR RESIDUE FE C 201
4	AC4	SOFTWARE	HIS D:14 , HIS D:40 , HIS D:46 , CYS D:110 , HIS D:113	BINDING SITE FOR RESIDUE FE D 201

(no "SS Bond" information available for 4BFK)

(no "Cis Peptide Bond" information available for 4BFK)

(no "SAP(SNP)/Variant" information available for 4BFK)

(no "PROSITE Motif" information available for 4BFK)

(no "Exon" information available for 4BFK)

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 A from PDB  Type:PROTEIN  Length:124
 aligned with SOR_ARCFU | O29903 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
            SOR_ARCFU     2 ELFQTADWKKEKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
               SCOP domains d4bfka_ A: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...........eeeeeeee..eeeeeee..............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bfk A   2 ELFQTADWKKQKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with SOR_ARCFU | O29903 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            SOR_ARCFU     1 MELFQTADWKKEKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
               SCOP domains d4bfkb_ B: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...........eeeeeeee..eeeeeee..............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bfk B   1 MELFQTADWKKQKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:125
 aligned with SOR_ARCFU | O29903 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            SOR_ARCFU     1 MELFQTADWKKEKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
               SCOP domains d4bfkc_ C: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..........eeeeeeee...eeeeeeee.............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bfk C   1 MELFQTADWKKQKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:PROTEIN  Length:125
 aligned with SOR_ARCFU | O29903 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            SOR_ARCFU     1 MELFQTADWKKEKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
               SCOP domains d4bfkd_ D: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..........eeeeeeeee..eeeeeeee.............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bfk D   1 MELFQTADWKKQKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Superoxide reductase-like (17)

Family: Superoxide reductase-like (13)

Protein domain: automated matches (6)

Archaeoglobus fulgidus [TaxId: 2234] (2)

1a	d4bfka_	A:
1b	d4bfkb_	B:
1c	d4bfkc_	C:
1d	d4bfkd_	D:

(no "CATH Domain" information available for 4BFK)

(no "Pfam Domain" information available for 4BFK)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (SOR_ARCFU | O29903)

molecular function
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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:0050605	superoxide reductase activity	Catalysis of the reaction: superoxide + reduced rubredoxin + 2 H+ = H2O2 + rubredoxin.
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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4bfk)

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	4bfk
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	1.15.1.2
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UniProtKB/Swiss-Prot
	SOR_ARCFU \| O29903	:	4bff 4bfj 4bgl 4c4b 4c4u

4bff	SUPEROXIDE REDUCTASE (NEELAREDOXIN) FROM ARCHAEOGLOBUS FULGIDUS IN THE REDUCED FORM
4bfj	SUPEROXIDE REDUCTASE (NEELAREDOXIN) FROM ARCHAEOGLOBUS FULGIDUS E12V MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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