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Title :   CRYSTAL STRUCTURE OF A MANGANESE SUPEROXIDE DISMUTASES FROM CAENORHABDITIS ELEGANS

Authors :   C. H. Trinh, T. Hunter, E. E. Stewart, S. E. V. Phillips, G. J. Hunter

Date :   03 Jun 08 (Deposition) - 09 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Alpha Hairpin N Domain, Alpha/Beta C Domain, Oxidoreductase, Manganese, Metal-Binding, Mitochondrion, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. H. Trinh, T. Hunter, E. E. Stewart, S. E. Phillips, G. J. Hunter
Purification, Crystallization And X-Ray Structures Of The Two Manganese Superoxide Dismutases From Caenorhabditis Elegans
Acta Crystallogr. , Sect. F V. 64 1110 2008
PubMed-ID: 19052361 | Reference-DOI: 10.1107/S1744309108037056

Molecule 1 - SUPEROXIDE DISMUTASE [MN] 1
	Chains	:	A, C
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC-99A
	Expression System Strain	:	OX326A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SOD-2, SDM-1, F10D11.1
	Organism Common	:	NEMATODE
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239

		1	2
Asymmetric Unit	:	A	C
Biological Unit 1 (2x)	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:26 , HIS A:74 , ASP A:158 , HIS A:162 , HOH A:202	BINDING SITE FOR RESIDUE MN A 198
2	AC2	SOFTWARE	TYR A:11 , GLN A:24 , GLN A:28 , HOH A:323 , LYS C:1 , SER C:3	BINDING SITE FOR RESIDUE SO4 A 199
3	AC3	SOFTWARE	HIS A:2 , SER A:3 , HIS A:71 , HOH A:288 , HOH A:419	BINDING SITE FOR RESIDUE SO4 A 200
4	AC4	SOFTWARE	HIS C:26 , HIS C:74 , ASP C:158 , HIS C:162 , HOH C:220	BINDING SITE FOR RESIDUE MN C 198
5	AC5	SOFTWARE	HIS C:2 , SER C:3 , HIS C:71 , HOH C:262 , HOH C:318 , HOH C:321 , HOH C:334	BINDING SITE FOR RESIDUE SO4 C 199

(no "SS Bond" information available for 3DC6)

Asymmetric Unit

No.	Residues
1	Glu A:15	-	Pro A:16
2	Glu C:15	-	Pro C:16

(no "SAP(SNP)/Variant" information available for 3DC6)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM1_CAEEL	182-189	2	A:158-165 C:158-165

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM1_CAEEL	182-189	4	A:158-165 C:158-165

(no "Exon" information available for 3DC6)

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:197
 aligned with SODM1_CAEEL | P31161 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:197
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
          SODM1_CAEEL    25 KHSLPDLPYDYADLEPVISHEIMQLHHQKHHATYVNNLNQIEEKLHEAVSKGNVKEAIALQPALKFNGGGHINHSIFWTNLAKDGGEPSAELLTAIKSDFGSLDNLQKQLSASTVAVQGSGWGWLGYCPKGKILKVATCANQDPLEATTGLVPLFGIDVWEHAYYLQYKNVRPDYVNAIWKIANWKNVSERFAKAQQ 221
               SCOP domains d3dc6a1 A:1-85 automated matches                                                     d3dc6a2 A:86-197 automated matches                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dc6 A   1 KHSLPDLPYDYADLEPVISHEIMQLHHQKHHATYVNNLNQIEEKLHEAVSKGNVKEAIALQPALKFNGGGHINHSIFWTNLAKDGGEPSAELLTAIKSDFGSLDNLQKQLSASTVAVQGSGWGWLGYCPKGKILKVATCANQDPLEATTGLVPLFGIDVWEHAYYLQYKNVRPDYVNAIWKIANWKNVSERFAKAQQ 197
                                    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:198
 aligned with SODM1_CAEEL | P31161 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:198
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        
          SODM1_CAEEL    24 SKHSLPDLPYDYADLEPVISHEIMQLHHQKHHATYVNNLNQIEEKLHEAVSKGNVKEAIALQPALKFNGGGHINHSIFWTNLAKDGGEPSAELLTAIKSDFGSLDNLQKQLSASTVAVQGSGWGWLGYCPKGKILKVATCANQDPLEATTGLVPLFGIDVWEHAYYLQYKNVRPDYVNAIWKIANWKNVSERFAKAQQ 221
               SCOP domains d3dc6c1 C:0-85 automated matches                                                      d3dc6c2 C:86-197 automated matches                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dc6 C   0 MKHSLPDLPYDYADLEPVISHEIMQLHHQKHHATYVNNLNQIEEKLHEAVSKGNVKEAIALQPALKFNGGGHINHSIFWTNLAKDGGEPSAELLTAIKSDFGSLDNLQKQLSASTVAVQGSGWGWLGYCPKGKILKVATCANQDPLEATTGLVPLFGIDVWEHAYYLQYKNVRPDYVNAIWKIANWKNVSERFAKAQQ 197
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

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 3DC6)

(no "Pfam Domain" information available for 3DC6)

Asymmetric Unit(hide GO term definitions)

Chain A,C (SODM1_CAEEL | P31161)

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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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.
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:0097249	mitochondrial respiratory chain supercomplex	A set of respiratory enzyme complexes of the mitochondrial inner membrane (including, for example, Complex II, Complex III, Complex IV, or F1-F0 ATPase) arranged to form a large supercomplex.
	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 Unit
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	Cis Peptide Bonds
		Glu A:15 - Pro A:16	[ RasMol ]
		Glu C:15 - Pro C:16	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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3dc5	HOMOLOGOUS PROTEIN

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