1UES - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS SOD

Authors :   F. Yamakura, S. Sugio, B. Y. Hiraoka, T. Yokota, D. Ohmori

Date :   20 May 03 (Deposition) - 20 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Metal-Specific, Cambialistic, Superoxide Dismutase, Sod, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Yamakura, S. Sugio, B. Y. Hiraoka, D. Ohmori, T. Yokota
Pronounced Conversion Of The Metal-Specific Activity Of Superoxide Dismutase From Porphyromonas Gingivalis By The Mutation Of A Single Amino Acid (Gly155Thr) Located Apart From The Active Site
Biochemistry V. 42 10790 2003
PubMed-ID: 12962504 | Reference-DOI: 10.1021/BI0349625
(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 Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	PORPHYROMONAS GINGIVALIS
	Organism Taxid	:	837
	Synonym	:	SOD

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) 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:193	BINDING SITE FOR RESIDUE MN A 192
2	AC2	SOFTWARE	HIS B:227 , HIS B:274 , ASP B:357 , HIS B:361 , HOH B:393	BINDING SITE FOR RESIDUE MN B 392
3	AC3	SOFTWARE	HOH C:3 , HIS C:427 , HIS C:474 , ASP C:557 , HIS C:561	BINDING SITE FOR RESIDUE MN C 592
4	AC4	SOFTWARE	HOH D:4 , HIS D:627 , HIS D:674 , ASP D:757 , HIS D:761	BINDING SITE FOR RESIDUE MN D 792

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

Asymmetric Unit

No.	Residues
1	Ala A:16	-	Pro A:17
2	Ala B:216	-	Pro B:217
3	Ala C:416	-	Pro C:417
4	Ala D:616	-	Pro D:617

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

Asymmetric 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:357-364 C:557-564 D:757-764

Biological Unit 1 (1, 2)

	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	2	A:157-164 B:357-364 - -

Biological Unit 2 (1, 2)

	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	2	- - C:557-564 D:757-764

(no "Exon" information available for 1UES)

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: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 d1uesa1 A:1-84 Cambialistic superoxide dismutase                                    d1uesa2 A:85-191 Cambialistic superoxide dismutase                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ues A   1 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLTFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 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 d1uesb1 B:201-284 Cambialistic superoxide dismutase                                 d1uesb2 B:285-391 Cambialistic superoxide dismutase                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ues B 201 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLTFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 391
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390

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 d1uesc1 C:401-484 Cambialistic superoxide dismutase                                 d1uesc2 C:485-591 Cambialistic superoxide dismutase                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ues C 401 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLTFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 591
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590

Chain D 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 d1uesd1 D:601-684 Cambialistic superoxide dismutase                                 d1uesd2 D:685-791 Cambialistic superoxide dismutase                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Sod_Fe_N-1uesD05 D:602-682                                                       ----Sod_Fe_C-1uesD01 D:687-791                                                                                Pfam domains (1)
           Pfam domains (2) -Sod_Fe_N-1uesD06 D:602-682                                                       ----Sod_Fe_C-1uesD02 D:687-791                                                                                Pfam domains (2)
           Pfam domains (3) -Sod_Fe_N-1uesD07 D:602-682                                                       ----Sod_Fe_C-1uesD03 D:687-791                                                                                Pfam domains (3)
           Pfam domains (4) -Sod_Fe_N-1uesD08 D:602-682                                                       ----Sod_Fe_C-1uesD04 D:687-791                                                                                Pfam domains (4)
         Sec.struct. author ...................hhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ues D 601 MTHELISLPYAVDALAPVISKETVEFHHGKHLKTYVDNLNKLIIGTEFENADLNTIVQKSEGGIFNNAGQTLNHNLYFTQFRPGKGGAPKGKLGEAIDKQFGSFEKFKEEFNTAGTTLFGSGWVWLASDANGKLSIEKEPNAGNPVRKGLNPLLTFDVWEHAYYLTYQNRRADHLKDLWSIVDWDIVESRY 791
                                   610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790

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 1UES)

Asymmetric 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-1uesD01	D:687-791
1b	Sod_Fe_C-1uesD02	D:687-791
1c	Sod_Fe_C-1uesD03	D:687-791
1d	Sod_Fe_C-1uesD04	D:687-791

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

Family: Sod_Fe_N (46)

Porphyromonas gingivalis (Bacteroides gingivalis) (3)

2a	Sod_Fe_N-1uesD05	D:602-682
2b	Sod_Fe_N-1uesD06	D:602-682
2c	Sod_Fe_N-1uesD07	D:602-682
2d	Sod_Fe_N-1uesD08	D:602-682

Asymmetric 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 Unit
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	Cis Peptide Bonds
		Ala A:16 - Pro A:17	[ RasMol ]
		Ala B:216 - Pro B:217	[ RasMol ]
		Ala C:416 - Pro C:417	[ RasMol ]
		Ala D:616 - Pro D:617	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	1ues
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	SODF_PORGI \| P19665
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	1.15.1.1
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	SODF_PORGI \| P19665
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UniProtKB/Swiss-Prot
	SODF_PORGI \| P19665	:	1qnn 1uer

1uer	THE SAME PROTEIN, WILD TYPE

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)

Sequences/Alignments

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SCOP Domains (2, 8)

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Gene Ontology (6, 6)

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