1ZUQ - JenaLib

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Title :   CONTRIBUTION TO STRUCTURE AND CATALYSIS OF TYROSINE 34 IN HUMAN MANGANESE SUPEROXIDE DISMUTASE

Authors :   A. S. Hearn, J. J. Perry, D. E. Cabelii, J. A. Tainer, H. S. Nick, D. S. Silv

Date :   31 May 05 (Deposition) - 02 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Mnsod, Manganese Superoxide Dismutase, Y34V Mutation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Perry, A. S. Hearn, D. E. Cabelli, H. S. Nick, J. A. Tainer, D. N. Silverman
Contribution Of Human Manganese Superoxide Dismutase Tyrosine 34 To Structure And Catalysis.
Biochemistry V. 48 3417 2009
PubMed-ID: 19265433 | Reference-DOI: 10.1021/BI8023288

Molecule 1 - SUPEROXIDE DISMUTASE
	Chains	:	A, B
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99A
	Expression System Strain	:	QC774I (SOD --)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (0, 0)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:26 , HIS A:74 , ASP A:159 , HIS A:163 , HOH A:5011	BINDING SITE FOR RESIDUE MN A 199
2	AC2	SOFTWARE	HIS B:26 , HIS B:74 , ASP B:159 , HIS B:163 , HOH B:5022	BINDING SITE FOR RESIDUE MN B 199

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

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)

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 d1zuqa1 A:1-83 Mn superoxide dismutase (MnSOD)                                     d1zuqa2 A:84-198 Mn superoxide dismutase (MnSOD)                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh 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)
                 1zuq A   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAVVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK 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 d1zuqb1 B:1-83 Mn superoxide dismutase (MnSOD)                                     d1zuqb2 B:84-198 Mn superoxide dismutase (MnSOD)                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Sod_Fe_N-1zuqB03 B:1-82                                                           ----Sod_Fe_C-1zuqB01 B:87-193                                                                                  ----- Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-1zuqB04 B:1-82                                                           ----Sod_Fe_C-1zuqB02 B:87-193                                                                                  ----- Pfam domains (2)
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh 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)
                 1zuq B   1 KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAVVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK 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 1ZUQ)

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-1zuqB01	B:87-193
1b	Sod_Fe_C-1zuqB02	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-1zuqB03	B:1-82
2b	Sod_Fe_N-1zuqB04	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
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	Cis Peptide Bonds
		Glu A:15 - Pro A:16	[ RasMol ]
		Glu B:15 - Pro B:16	[ RasMol ]

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Access by PDB/NDB ID
	1zuq
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	SODM_HUMAN \| P04179
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	1.15.1.1
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	0129
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	0130
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1zsp	CONTRIBUTION TO STRUCTURE AND CATALYSIS OF TYROSINE 34 IN HUMAN MANGANESE SUPEROXIDE DISMUTASE
1zte	CONTRIBUTION TO STRUCTURE AND CATALYSIS OF TYROSINE 34 IN HUMAN MANGANESE SUPEROXIDE DISMUTASE

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

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Exons (4, 8)

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