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Asym./Biol. Unit (Jmol Viewer)

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Title :   CAMBIALISTIC SUPEROXIDE DISMUTASE FROM PORPHYROMONAS GINGIVALIS

Authors :   S. Sugio, B. Y. Hiraoka, F. Yamakura

Date :   20 Oct 99 (Deposition) - 21 Jun 00 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

Reference :   S. Sugio, B. Y. Hiraoka, F. Yamakura
Crystal Structure Of Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis
Eur. J. Biochem. V. 267 3487 2000
PubMed-ID: 10848964 | Reference-DOI: 10.1046/J.1432-1327.2000.01373.X
(for further references see the PDB file header)

Molecule 1 - SUPEROXIDE DISMUTASE
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	QC774
	Expression System Gene	:	SOD
	Expression System Plasmid	:	PKD210
	Expression System Taxid	:	562
	Organism Scientific	:	PORPHYROMONAS GINGIVALIS
	Organism Taxid	:	837
	Other Details	:	EACH CHAIN CONTAINS ONE METAL ION (FE3+:MN3+=3:1).
	Synonym	:	FE/MN-SOD

		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:27 , HIS A:74 , ASP A:157 , HIS A:161 , HOH A:2085	BINDING SITE FOR RESIDUE FE A 201
2	AC2	SOFTWARE	HIS B:27 , HIS B:74 , ASP B:157 , HIS B:161 , HOH B:2088	BINDING SITE FOR RESIDUE FE B 201
3	AC3	SOFTWARE	HIS C:27 , HIS C:74 , ASP C:157 , HIS C:161 , HOH C:2117	BINDING SITE FOR RESIDUE FE C 201
4	AC4	SOFTWARE	HIS D:27 , HIS D:74 , ASP D:157 , HIS D:161 , HOH D:2056	BINDING SITE FOR RESIDUE FE D 201

(no "SS Bond" information available for 1QNN)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:16	-	Pro A:17
2	Ala B:16	-	Pro B:17
3	Ala C:16	-	Pro C:17
4	Ala D:16	-	Pro D:17

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODF_PORGI	157-164	4	A:157-164 B:157-164 C:157-164 D:157-164

(no "Exon" information available for 1QNN)

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:191
 aligned with SODF_PORGI | P19665 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           SODF_PORGI     1 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLGFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 191
               SCOP domains d1qnna1 A:1-84 Cambialistic superoxide dismutase                                    d1qnna2 A:85-191 Cambialistic superoxide dismutase                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qnn A   1 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLGFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with SODF_PORGI | P19665 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           SODF_PORGI     1 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLGFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 191
               SCOP domains d1qnnb1 B:1-84 Cambialistic superoxide dismutase                                    d1qnnb2 B:85-191 Cambialistic superoxide dismutase                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qnn B   1 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLGFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain C from PDB  Type:PROTEIN  Length:191
 aligned with SODF_PORGI | P19665 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           SODF_PORGI     1 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLGFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 191
               SCOP domains d1qnnc1 C:1-84 Cambialistic superoxide dismutase                                    d1qnnc2 C:85-191 Cambialistic superoxide dismutase                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qnn C   1 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLGFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain D from PDB  Type:PROTEIN  Length:190
 aligned with SODF_PORGI | P19665 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
           SODF_PORGI     2 THELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLGFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 191
               SCOP domains d1qnnd1 D:2-84 Cambialistic superoxide dismutase                                   d1qnnd2 D:85-191 Cambialistic superoxide dismutase                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Sod_Fe_N-1qnnD05 D:2-82                                                          ----Sod_Fe_C-1qnnD01 D:87-191                                                                                 Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-1qnnD06 D:2-82                                                          ----Sod_Fe_C-1qnnD02 D:87-191                                                                                 Pfam domains (2)
           Pfam domains (3) Sod_Fe_N-1qnnD07 D:2-82                                                          ----Sod_Fe_C-1qnnD03 D:87-191                                                                                 Pfam domains (3)
           Pfam domains (4) Sod_Fe_N-1qnnD08 D:2-82                                                          ----Sod_Fe_C-1qnnD04 D:87-191                                                                                 Pfam domains (4)
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qnn D   2 THELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLGFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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 '\|'

(no "CATH Domain" information available for 1QNN)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Sod_Fe_C] (46)

Family: Sod_Fe_C (46)

Porphyromonas gingivalis (Bacteroides gingivalis) (3)

1a	Sod_Fe_C-1qnnD01	D:87-191
1b	Sod_Fe_C-1qnnD02	D:87-191
1c	Sod_Fe_C-1qnnD03	D:87-191
1d	Sod_Fe_C-1qnnD04	D:87-191

Clan: no clan defined [family: Sod_Fe_N] (46)

Family: Sod_Fe_N (46)

Porphyromonas gingivalis (Bacteroides gingivalis) (3)

2a	Sod_Fe_N-1qnnD05	D:2-82
2b	Sod_Fe_N-1qnnD06	D:2-82
2c	Sod_Fe_N-1qnnD07	D:2-82
2d	Sod_Fe_N-1qnnD08	D:2-82

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (SODF_PORGI | P19665)

molecular function
	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:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
	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:0019430	removal of superoxide radicals	Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
	GO:0006801	superoxide metabolic process	The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:16 - Pro A:17	[ RasMol ]
		Ala B:16 - Pro B:17	[ RasMol ]
		Ala C:16 - Pro C:17	[ RasMol ]
		Ala D:16 - Pro D:17	[ RasMol ]

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	1qnn
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	SODF_PORGI \| P19665
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	1.15.1.1
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	SODF_PORGI \| P19665	:	1uer 1ues

(no "Related Entries Specified in the PDB File" available for 1QNN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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