1VAR - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   MITOCHONDRIAL MANGANESE SUPEROXIDE DISMUTASE VARIANT WITH ILE 58 REPLACED BY THR

Authors :   G. E. O. Borgstahl, H. E. Parge, J. A. Tainer

Date :   04 Jan 96 (Deposition) - 10 Jun 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Oxidoreductase, Manganese, Mitochondrion, Transit Peptide, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. E. Borgstahl, H. E. Parge, M. J. Hickey, M. J. Johnson, M. Boissinot, R. A. Hallewell, J. R. Lepock, D. E. Cabelli, J. A. Tainer
Human Mitochondrial Manganese Superoxide Dismutase Polymorphic Variant Ile58Thr Reduces Activity By Destabilizing The Tetrameric Interface.
Biochemistry V. 35 4287 1996
PubMed-ID: 8605177 | Reference-DOI: 10.1021/BI951892W
(for further references see the PDB file header)

Molecule 1 - MANGANESE SUPEROXIDE DISMUTASE
	Chains	:	A, B
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	HUMAN KIDNEY SOD2
	Expression System Strain	:	SODASODB
	Expression System Taxid	:	562
	Gene	:	HUMAN KIDNEY SOD2
	Mutation	:	YES
	Organ	:	KIDNEY
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MN3	2	Ligand/Ion	MANGANESE (III) ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MN3	4	Ligand/Ion	MANGANESE (III) 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 , HOH A:200	BINDING SITE FOR RESIDUE MN3 A 199
2	AC2	SOFTWARE	HIS B:26 , HIS B:74 , ASP B:159 , HIS B:163 , HOH B:200	BINDING SITE FOR RESIDUE MN3 B 199
3	MNA	UNKNOWN	MN3 A:199 , HIS A:26 , HIS A:74 , ASP A:159 , HIS A:163 , HOH A:200	NULL
4	MNB	UNKNOWN	MN3 B:199 , HIS B:26 , HIS B:74 , ASP B:159 , HIS B:163 , HOH B:200	NULL

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

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	T	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	T	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)

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

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:151-198 B:151-198	48 48
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:198
 aligned with SODM_HUMAN | P04179 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:198
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
           SODM_HUMAN    25 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK 222
               SCOP domains d1vara1 A:1-83 Mn superoxide dismutase (MnSOD)                                     d1vara2 A:84-198 Mn superoxide dismutase (MnSOD)                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh.hhhhhhhhhhhhhh.....eeeeeeee....eeeeeeee....hhhhhheeeeeeee.............hhhhhhhh....hhhhhhhhhhhhh. 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:151-198 UniProt: 175-222       Transcript 1 (2)
                 1var A   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQTALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK 198
                                    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:198
 aligned with SODM_HUMAN | P04179 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:198
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
           SODM_HUMAN    25 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK 222
               SCOP domains d1varb1 B:1-83 Mn superoxide dismutase (MnSOD)                                     d1varb2 B:84-198 Mn superoxide dismutase (MnSOD)                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Sod_Fe_N-1varB03 B:1-82                                                           ----Sod_Fe_C-1varB01 B:87-193                                                                                  ----- Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-1varB04 B:1-82                                                           ----Sod_Fe_C-1varB02 B:87-193                                                                                  ----- Pfam domains (2)
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh.hhhhhhhhhhhhhh.....eeeeeeee....eeeeeeee....hhhhhheeeeeeee.............hhhhhhhh....hhhhhhhhhhhhh. 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:151-198 UniProt: 175-222       Transcript 1 (2)
                 1var B   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQTALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK 198
                                    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 1VAR)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Sod_Fe_C (46)

Homo sapiens (Human) (17)

1a	Sod_Fe_C-1varB01	B:87-193
1b	Sod_Fe_C-1varB02	B:87-193

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

Family: Sod_Fe_N (46)

Homo sapiens (Human) (17)

2a	Sod_Fe_N-1varB03	B:1-82
2b	Sod_Fe_N-1varB04	B:1-82

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MN3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		MNA	[ RasMol ]	+environment [ RasMol ]
		MNB	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:15 - Pro A:16	[ RasMol ]
		Glu B:15 - Pro B:16	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1var
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SODM_HUMAN \| P04179
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.15.1.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	0129
		Age Related Information	:	GenAge
	0130
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SODM_HUMAN \| P04179
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

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)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (23, 23)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File