1Y67 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MANGANESE SUPEROXIDE DISMUTASE FROM DEINOCOCCUS RADIODURANS

Authors :   S. Chan, S. Tanaka, M. R. Sawaya, L. J. Perry

Date :   03 Dec 04 (Deposition) - 21 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Superoxide Dismutase, Manganese Enzyme, Metalloprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chan, S. Tanaka, M. R. Sawaya, L. J. Perry
Crystal Structure Of Manganese Superoxide Dismutase From Deinococcus Radiodurans
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - MANGANESE SUPEROXIDE DISMUTASE
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21-GOLD (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SODA
	Organism Scientific	:	DEINOCOCCUS RADIODURANS
	Organism Taxid	:	1299
	Synonym	:	MNSOD

		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	FE	4	Ligand/Ion	FE (III) ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:27 , HIS A:81 , ASP A:173 , HIS A:177 , HOH A:233	BINDING SITE FOR RESIDUE FE A 229
2	AC2	SOFTWARE	HIS B:27 , HIS B:81 , ASP B:173 , HIS B:177 , HOH B:230	BINDING SITE FOR RESIDUE FE B 229
3	AC3	SOFTWARE	HIS C:27 , HIS C:81 , ASP C:173 , HIS C:177 , HOH C:230	BINDING SITE FOR RESIDUE FE C 229
4	AC4	SOFTWARE	HIS D:27 , HIS D:81 , ASP D:173 , HIS D:177 , HOH D:234	BINDING SITE FOR RESIDUE FE D 229

(no "SS Bond" information available for 1Y67)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 1Y67)

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.	SODM_DEIRA	173-180	4	A:173-180 B:173-180 C:173-180 D:173-180

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.	SODM_DEIRA	173-180	2	A:173-180 B:173-180 - -

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.	SODM_DEIRA	173-180	2	- - C:173-180 D:173-180

(no "Exon" information available for 1Y67)

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:210
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:213
                                                                                                                                                                                                                                            211  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210|  
           SODM_DEIRA     1 MAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK--   -
               SCOP domains -d1y67a1 A:2-89 Mn superoxide dismutase (MnSOD)                                          --------d1y67a2 A:98-213 Mn superoxide dismutase (MnSOD)                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh......---....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y67 A   1 AAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQG---ANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAKLV 213
                                    10        20        30        40        50        60        70        80        90  |   |100       110       120       130       140       150       160       170       180       190       200       210   
                                                                                                                       93  97

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SODM_DEIRA     1 MAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 211
               SCOP domains -d1y67b1 B:2-89 Mn superoxide dismutase (MnSOD)                                          --------d1y67b2 B:98-211 Mn superoxide dismutase (MnSOD)                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.........hhhhhhhhhhhhhhhhhhhhh...-------...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhh...........hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y67 B   1 AAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQ-------NQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
                                                                                                                    90      98

Chain C from PDB  Type:PROTEIN  Length:204
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:212
                                                                                                                                                                                                                                           211  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
           SODM_DEIRA     2 AYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK--   -
               SCOP domains d1y67c1 C:2-89 Mn superoxide dismutase (MnSOD)                                          --------d1y67c2 C:98-213 Mn superoxide dismutase (MnSOD)                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..--------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh...........hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y67 C   2 AYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMG--------NQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAKLV 213
                                    11        21        31        41        51        61        71        81       | -      |101       111       121       131       141       151       161       171       181       191       201       211  
                                                                                                                  89       98

Chain D from PDB  Type:PROTEIN  Length:214
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:214
                                                                                                                                                                                                                                           211    
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
           SODM_DEIRA     2 AYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK----   -
               SCOP domains d1y67d1 D:2-89 Mn superoxide dismutase (MnSOD)                                          --------d1y67d2 D:98-213 Mn superoxide dismutase (MnSOD)                                                                    -- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Sod_Fe_N-1y67D05 D:2-89                                                                 --------Sod_Fe_C-1y67D01 D:98-207                                                                                     -------- Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-1y67D06 D:2-89                                                                 --------Sod_Fe_C-1y67D02 D:98-207                                                                                     -------- Pfam domains (2)
           Pfam domains (3) Sod_Fe_N-1y67D07 D:2-89                                                                 --------Sod_Fe_C-1y67D03 D:98-207                                                                                     -------- Pfam domains (3)
           Pfam domains (4) Sod_Fe_N-1y67D08 D:2-89                                                                 --------Sod_Fe_C-1y67D04 D:98-207                                                                                     -------- Pfam domains (4)
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh...........hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y67 D   2 AYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAKLVPR 215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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 1Y67)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Sod_Fe_C (46)

Deinococcus radiodurans (2)

1a	Sod_Fe_C-1y67D01	D:98-207
1b	Sod_Fe_C-1y67D02	D:98-207
1c	Sod_Fe_C-1y67D03	D:98-207
1d	Sod_Fe_C-1y67D04	D:98-207

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

Family: Sod_Fe_N (46)

Deinococcus radiodurans (2)

2a	Sod_Fe_N-1y67D05	D:2-89
2b	Sod_Fe_N-1y67D06	D:2-89
2c	Sod_Fe_N-1y67D07	D:2-89
2d	Sod_Fe_N-1y67D08	D:2-89

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SODM_DEIRA | Q9RUV2)

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
		Glu A:16 - Pro A:17	[ RasMol ]
		Glu B:16 - Pro B:17	[ RasMol ]
		Glu C:16 - Pro C:17	[ RasMol ]
		Glu D:16 - Pro D:17	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	1y67
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	SODM_DEIRA \| Q9RUV2	:	2aw9 2cdy 2ce4 3kky

(no "Related Entries Specified in the PDB File" available for 1Y67)

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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