3C3T - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   ROLE OF A GLUTAMATE BRIDGE SPANNING THE DIMERIC INTERFACE OF HUMAN MANGANESE SUPEROXIDE DISMUTASE

Authors :   P. S. Quint, J. F. Domsic, D. E. Cabelli, R. Mckenna, D. N. Silverman

Date :   28 Jan 08 (Deposition) - 22 Apr 08 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: B  (2x)
Biol. Unit 4: A  (2x)

Keywords :   Metalloenzyme, Manganese, Metal-Binding, Mitochondrion, Oxidoreductase, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. S. Quint, J. F. Domsic, D. E. Cabelli, R. Mckenna, D. N. Silverman
Role Of A Glutamate Bridge Spanning The Dimeric Interface O Human Manganese Superoxide Dismutase.
Biochemistry V. 47 4621 2008
PubMed-ID: 18373354 | Reference-DOI: 10.1021/BI7024518

Molecule 1 - SUPEROXIDE DISMUTASE [MN]
	Chains	:	A, B
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	QC774
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 25-222
	Gene	:	SOD2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

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

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

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

Biological Unit 3 (1, 2)

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

Biological Unit 4 (1, 2)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:26 , HIS A:74 , ASP A:159 , HIS A:163	BINDING SITE FOR RESIDUE MN A 199
2	AC2	SOFTWARE	HIS B:26 , HIS B:74 , ASP B:159 , HIS B:163	BINDING SITE FOR RESIDUE MN B 199
3	AC3	SOFTWARE	HIS A:30 , TYR A:34 , TRP A:161 , HIS A:163	BINDING SITE FOR RESIDUE SO4 A 501
4	AC4	SOFTWARE	HIS B:30 , TYR B:34 , TRP B:161 , HIS B:163	BINDING SITE FOR RESIDUE SO4 B 502

(no "SS Bond" information available for 3C3T)

Asymmetric Unit

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

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_019364	E	66	V	SODM_HUMAN	Polymorphism	5746097	A/B	E	42	V
2	UniProt	VAR_025898	G	76	R	SODM_HUMAN	Polymorphism	4987023	A/B	G	52	R
3	UniProt	VAR_007165	I	82	T	SODM_HUMAN	Polymorphism	1141718	A/B	I	58	T
4	UniProt	VAR_019365	R	156	W	SODM_HUMAN	Polymorphism	5746129	A/B	R	132	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (4, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_019364	E	66	V	SODM_HUMAN	Polymorphism	5746097	A/B	E	42	V
2	UniProt	VAR_025898	G	76	R	SODM_HUMAN	Polymorphism	4987023	A/B	G	52	R
3	UniProt	VAR_007165	I	82	T	SODM_HUMAN	Polymorphism	1141718	A/B	I	58	T
4	UniProt	VAR_019365	R	156	W	SODM_HUMAN	Polymorphism	5746129	A/B	R	132	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_019364	E	66	V	SODM_HUMAN	Polymorphism	5746097	A/B	E	42	V
2	UniProt	VAR_025898	G	76	R	SODM_HUMAN	Polymorphism	4987023	A/B	G	52	R
3	UniProt	VAR_007165	I	82	T	SODM_HUMAN	Polymorphism	1141718	A/B	I	58	T
4	UniProt	VAR_019365	R	156	W	SODM_HUMAN	Polymorphism	5746129	A/B	R	132	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_019364	E	66	V	SODM_HUMAN	Polymorphism	5746097	B	E	42	V
2	UniProt	VAR_025898	G	76	R	SODM_HUMAN	Polymorphism	4987023	B	G	52	R
3	UniProt	VAR_007165	I	82	T	SODM_HUMAN	Polymorphism	1141718	B	I	58	T
4	UniProt	VAR_019365	R	156	W	SODM_HUMAN	Polymorphism	5746129	B	R	132	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_019364	E	66	V	SODM_HUMAN	Polymorphism	5746097	A	E	42	V
2	UniProt	VAR_025898	G	76	R	SODM_HUMAN	Polymorphism	4987023	A	G	52	R
3	UniProt	VAR_007165	I	82	T	SODM_HUMAN	Polymorphism	1141718	A	I	58	T
4	UniProt	VAR_019365	R	156	W	SODM_HUMAN	Polymorphism	5746129	A	R	132	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	SODM_HUMAN	183-190	2	A:159-166 B:159-166

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.	SODM_HUMAN	183-190	4	A:159-166 B:159-166

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_HUMAN	183-190	2	A:159-166 B:159-166

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_HUMAN	183-190	2	- B:159-166

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODM_HUMAN	183-190	2	A:159-166 -

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000367055	1b	ENSE00001872926	chr6:160114352-160114177	176	SODM_HUMAN	1-8	8	0	-	-
1.2a	ENST00000367055	2a	ENSE00000815316	chr6:160113895-160113693	203	SODM_HUMAN	8-76	69	2	A:1-52 B:1-52	52 52
1.3	ENST00000367055	3	ENSE00000765625	chr6:160109274-160109158	117	SODM_HUMAN	76-115	40	2	A:52-91 B:52-91	40 40
1.4	ENST00000367055	4	ENSE00000765624	chr6:160106065-160105886	180	SODM_HUMAN	115-175	61	2	A:91-151 B:91-151	61 61
1.5a	ENST00000367055	5a	ENSE00001431742	chr6:160103670-160103506	165	SODM_HUMAN	175-222	48	2	A:151-196 B:151-196	46 46
1.6b	ENST00000367055	6b	ENSE00001926068	chr6:160100330-160100148	183	SODM_HUMAN	-	0	0	-	-

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:196
 aligned with SODM_HUMAN | P04179 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:196
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214      
           SODM_HUMAN    25 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMAC 220
               SCOP domains d3c3ta1 A:1-83 Mn superoxide dismutase (MnSOD)                                     d3c3ta2 A:84-196 Mn superoxide dismutase (MnSOD)                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------V---------R-----T-------------------------------------------------------------------------W---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:1-52 UniProt: 8-76 [INCOMPLETE]   --------------------------------------Exon 1.4  PDB: A:91-151 UniProt: 115-175                     --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.3  PDB: A:52-91 UniProt: 76-115  -----------------------------------------------------------Exon 1.5a  PDB: A:151-196 UniProt: 175-222     Transcript 1 (2)
                 3c3t A   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWDHAYYLQYKNVRPDYLKAIWNVINWENVTERYMAC 196
                                    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:196
 aligned with SODM_HUMAN | P04179 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:196
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214      
           SODM_HUMAN    25 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMAC 220
               SCOP domains d3c3tb1 B:1-83 Mn superoxide dismutase (MnSOD)                                     d3c3tb2 B:84-196 Mn superoxide dismutase (MnSOD)                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------V---------R-----T-------------------------------------------------------------------------W---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:1-52 UniProt: 8-76 [INCOMPLETE]   --------------------------------------Exon 1.4  PDB: B:91-151 UniProt: 115-175                     --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.3  PDB: B:52-91 UniProt: 76-115  -----------------------------------------------------------Exon 1.5a  PDB: B:151-196 UniProt: 175-222     Transcript 1 (2)
                 3c3t B   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWDHAYYLQYKNVRPDYLKAIWNVINWENVTERYMAC 196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

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 3C3T)

(no "Pfam Domain" information available for 3C3T)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SODM_HUMAN | P04179)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	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:0003069	acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure	The process in which acetylcholine signaling causes vasodilation, resulting in a change in blood pressure.
	GO:0001315	age-dependent response to reactive oxygen species	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.) as a result of reactive oxygen species, where the change varies according to the age of the cell or organism.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0043524	negative regulation of neuron apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
	GO:1902176	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of an oxidative stress-induced intrinsic apoptotic signaling pathway.
	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:0032364	oxygen homeostasis	A homeostatic process involved in the maintenance of an internal steady state of oxygen within an organism or cell.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0008217	regulation of blood pressure	Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0001836	release of cytochrome c from mitochondria	The process that results in the movement of cytochrome c from the mitochondrial intermembrane space into the cytosol, which is part of the apoptotic signaling pathway and leads to caspase activation.
	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:0000302	response to reactive oxygen species	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.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
	GO:0000303	response to superoxide	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.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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 Unit
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Access by PDB/NDB ID
	3c3t
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3c3s	SAME PROTEIN MUTATION WITH E162A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

PROSITE Motifs (1, 2)

Exons (4, 8)

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SCOP Domains (2, 4)

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