3LSU - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF SOD2 FROM SACCHAROMYCES CEREVISIAE

Authors :   Y. Sheng, D. Cascio, J. S. Valentine

Date :   12 Feb 10 (Deposition) - 23 Feb 11 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Mn Superoxide Dismutase, Reductive Methylation, Manganese, Metal- Binding, Mitochondrion, Oxidoreductase, Phosphoprotein, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Sheng, D. Cascio, J. S. Valentine
Crystal Structure Of Sod2 From Saccharomyces Cerevisiae
To Be Published
PubMed: search

Molecule 1 - SUPEROXIDE DISMUTASE [MN], MITOCHONDRIAL
	Chains	:	A, B, C, D
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	YEAST
	Expression System Plasmid	:	YEP352-SOD2
	Expression System Strain	:	EG103
	Expression System Taxid	:	4932
	Expression System Vector Type	:	PLASMID
	Gene	:	SOD2, YHR008C
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 73)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MLY	64	Mod. Amino Acid	N-DIMETHYL-LYSINE
3	MN	4	Ligand/Ion	MANGANESE (II) ION
4	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:26 , HIS A:81 , ASP A:168 , HIS A:172 , HOH A:211	BINDING SITE FOR RESIDUE MN A 208
2	AC2	SOFTWARE	HIS B:26 , HIS B:81 , ASP B:168 , HIS B:172 , HOH B:214	BINDING SITE FOR RESIDUE MN B 208
3	AC3	SOFTWARE	MLY A:8 , GLN A:93 , ASN A:194 , HOH B:230	BINDING SITE FOR RESIDUE GOL B 209
4	AC4	SOFTWARE	HIS C:26 , HIS C:81 , ASP C:168 , HIS C:172 , HOH C:212	BINDING SITE FOR RESIDUE MN C 208
5	AC5	SOFTWARE	GLN C:177 , GLN C:179 , GOL C:210 , HOH C:222 , HOH C:259	BINDING SITE FOR RESIDUE NA C 209
6	AC6	SOFTWARE	GLY A:12 , GLU A:15 , GLN C:177 , TYR C:178 , MLY C:181 , ASP C:184 , NA C:209 , HOH C:259	BINDING SITE FOR RESIDUE GOL C 210
7	AC7	SOFTWARE	HIS D:26 , HIS D:81 , ASP D:168 , HIS D:172 , HOH D:214	BINDING SITE FOR RESIDUE MN D 208
8	AC8	SOFTWARE	GLU B:15 , GLY B:20 , GLN B:21 , TYR D:178 , MLY D:181 , ASP D:184 , HOH D:257	BINDING SITE FOR RESIDUE GOL D 209
9	AC9	SOFTWARE	GLU B:15 , PRO B:16 , ILE B:18 , SER B:19 , GLN B:177 , PRO D:16	BINDING SITE FOR RESIDUE GOL D 210

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:15	-	Pro A:16
2	Glu B:15	-	Pro B:16
3	Glu C:15	-	Pro C:16
4	Glu D:15	-	Pro D:16

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

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.	SODM_YEAST	194-201	4	A:168-175 B:168-175 C:168-175 D:168-175

(no "Exon" information available for 3LSU)

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:206
 aligned with SODM_YEAST | P00447 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:206
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226      
           SODM_YEAST    27 KVTLPDLKWDFGALEPYISGQINELHYTKHHQTYVNGFNTAVDQFQELSDLLAKEPSPANARKMIAIQQNIKFHGGGFTNHCLFWENLAPESQGGGEPPTGALAKAIDEQFGSLDELIKLTNTKLAGVQGSGWAFIVKNLSNGGKLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNKKADYFKAIWNVVNWKEASRRFDAGK 232
               SCOP domains d3lsua1 A:1-90 automated matches                                                          d3lsua2 A:91-206 automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeee........eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lsu A   1 kVTLPDLkWDFGALEPYISGQINELHYTkHHQTYVNGFNTAVDQFQELSDLLAkEPSPANARkMIAIQQNIkFHGGGFTNHCLFWENLAPESQGGGEPPTGALAkAIDEQFGSLDELIkLTNTkLAGVQGSGWAFIVkNLSNGGkLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNkkADYFkAIWNVVNWkEASRRFDAGk 206
                            |      |10        20        30        40        50   |    60  |     70 |      80        90       100    |  110       120   |   130       140    |  150       160       170       180||    |190     | 200     |
                            |      8-MLY               29-MLY                   54-MLY   63-MLY   72-MLY                          105-MLY       119-MLY|           138-MLY  |                                 181-MLY |      196-MLY   206-MLY
                            1-MLY                                                                                                                    124-MLY              145-MLY                              182-MLY|                   
                                                                                                                                                                                                                    187-MLY

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with SODM_YEAST | P00447 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:207
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       
           SODM_YEAST    27 KVTLPDLKWDFGALEPYISGQINELHYTKHHQTYVNGFNTAVDQFQELSDLLAKEPSPANARKMIAIQQNIKFHGGGFTNHCLFWENLAPESQGGGEPPTGALAKAIDEQFGSLDELIKLTNTKLAGVQGSGWAFIVKNLSNGGKLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNKKADYFKAIWNVVNWKEASRRFDAGKI 233
               SCOP domains d3lsub1 B:1-90 automated matches                                                          d3lsub2 B:91-207 automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhh..eeeeeee........eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lsu B   1 kVTLPDLkWDFGALEPYISGQINELHYTkHHQTYVNGFNTAVDQFQELSDLLAkEPSPANARkMIAIQQNIkFHGGGFTNHCLFWENLAPESQGGGEPPTGALAkAIDEQFGSLDELIkLTNTkLAGVQGSGWAFIVkNLSNGGkLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNkkADYFkAIWNVVNWkEASRRFDAGkI 207
                            |      |10        20        30        40        50   |    60  |     70 |      80        90       100    |  110       120   |   130       140    |  150       160       170       180||    |190     | 200     | 
                            |      8-MLY               29-MLY                   54-MLY   63-MLY   72-MLY                          105-MLY       119-MLY|           138-MLY  |                                 181-MLY |      196-MLY   206-MLY
                            1-MLY                                                                                                                    124-MLY              145-MLY                              182-MLY|                    
                                                                                                                                                                                                                    187-MLY

Chain C from PDB  Type:PROTEIN  Length:206
 aligned with SODM_YEAST | P00447 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:206
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226      
           SODM_YEAST    27 KVTLPDLKWDFGALEPYISGQINELHYTKHHQTYVNGFNTAVDQFQELSDLLAKEPSPANARKMIAIQQNIKFHGGGFTNHCLFWENLAPESQGGGEPPTGALAKAIDEQFGSLDELIKLTNTKLAGVQGSGWAFIVKNLSNGGKLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNKKADYFKAIWNVVNWKEASRRFDAGK 232
               SCOP domains d3lsuc1 C:1-90 automated matches                                                          d3lsuc2 C:91-206 automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee......eeeeeee........eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lsu C   1 kVTLPDLkWDFGALEPYISGQINELHYTkHHQTYVNGFNTAVDQFQELSDLLAkEPSPANARkMIAIQQNIkFHGGGFTNHCLFWENLAPESQGGGEPPTGALAkAIDEQFGSLDELIkLTNTkLAGVQGSGWAFIVkNLSNGGkLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNkkADYFkAIWNVVNWkEASRRFDAGk 206
                            |      |10        20        30        40        50   |    60  |     70 |      80        90       100    |  110       120   |   130       140    |  150       160       170       180||    |190     | 200     |
                            |      8-MLY               29-MLY                   54-MLY   63-MLY   72-MLY                          105-MLY       119-MLY|           138-MLY  |                                 181-MLY |      196-MLY   206-MLY
                            1-MLY                                                                                                                    124-MLY              145-MLY                              182-MLY|                   
                                                                                                                                                                                                                    187-MLY

Chain D from PDB  Type:PROTEIN  Length:207
 aligned with SODM_YEAST | P00447 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:207
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       
           SODM_YEAST    27 KVTLPDLKWDFGALEPYISGQINELHYTKHHQTYVNGFNTAVDQFQELSDLLAKEPSPANARKMIAIQQNIKFHGGGFTNHCLFWENLAPESQGGGEPPTGALAKAIDEQFGSLDELIKLTNTKLAGVQGSGWAFIVKNLSNGGKLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNKKADYFKAIWNVVNWKEASRRFDAGKI 233
               SCOP domains d3lsud1 D:1-90 automated matches                                                          d3lsud2 D:91-207 automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Sod_Fe_N-3lsuD05 D:1-89                                                                  ------Sod_Fe_C-3lsuD01 D:96-202                                                                                  ----- Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-3lsuD06 D:1-89                                                                  ------Sod_Fe_C-3lsuD02 D:96-202                                                                                  ----- Pfam domains (2)
           Pfam domains (3) Sod_Fe_N-3lsuD07 D:1-89                                                                  ------Sod_Fe_C-3lsuD03 D:96-202                                                                                  ----- Pfam domains (3)
           Pfam domains (4) Sod_Fe_N-3lsuD08 D:1-89                                                                  ------Sod_Fe_C-3lsuD04 D:96-202                                                                                  ----- Pfam domains (4)
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeee........eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lsu D   1 kVTLPDLkWDFGALEPYISGQINELHYTkHHQTYVNGFNTAVDQFQELSDLLAkEPSPANARkMIAIQQNIkFHGGGFTNHCLFWENLAPESQGGGEPPTGALAkAIDEQFGSLDELIkLTNTkLAGVQGSGWAFIVkNLSNGGkLDVVQTYNQDTVTGPLVPLVAIDAWEHAYYLQYQNkkADYFkAIWNVVNWkEASRRFDAGkI 207
                            |      |10        20        30        40        50   |    60  |     70 |      80        90       100    |  110       120   |   130       140    |  150       160       170       180||    |190     | 200     | 
                            |      8-MLY               29-MLY                   54-MLY   63-MLY   72-MLY                          105-MLY       119-MLY|           138-MLY  |                                 181-MLY |      196-MLY   206-MLY
                            1-MLY                                                                                                                    124-MLY              145-MLY                              182-MLY|                    
                                                                                                                                                                                                                    187-MLY

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 3LSU)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (SODM_YEAST | P00447)

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:0001324	age-dependent response to oxidative stress involved in chronological cell aging	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) occurring in non-dividing cells as they age as a result of oxidative stress, where the change varies according to the age of the cell or organism.
	GO:0001320	age-dependent response to reactive oxygen species involved in chronological cell aging	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) occurring in non-dividing cells as they age as a result of reactive oxygen species, where the change varies according to the age of the cell or organism.
	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:0072593	reactive oxygen species metabolic process	The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
	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:0001302	replicative cell aging	The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.
	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.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu A:15 - Pro A:16	[ RasMol ]
		Glu B:15 - Pro B:16	[ RasMol ]
		Glu C:15 - Pro C:16	[ RasMol ]
		Glu D:15 - Pro D:16	[ RasMol ]

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	3lsu
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	SODM_YEAST \| P00447	:	3bfr 3rn4 4e4e 4f6e

3bfr	OUR ENTRY IS THE SAME PROTEIN BUT WITH MN(II) INSTEAD OF MN(III) IN 3BFR. OUR ENTRY HAS THE LYSINES METHYLATED

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 73)

Sites (9, 9)

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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SCOP Domains (2, 8)

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