1GN3 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   H145Q MUTANT OF MYCOBACTERIUM TUBERCULOSIS IRON-SUPEROXIDE DISMUTASE.

Authors :   K. A. Bunting, J. B. Cooper, M. O. Badasso, I. J. Tickle, M. Newton, S. P. Wood, Y. Zhang, D. B. Young

Date :   02 Oct 01 (Deposition) - 05 Oct 01 (Release) - 01 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.00

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

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. A. Bunting, J. B. Cooper, M. O. Badasso, I. J. Tickle, M. Newton, S. P. Wood, D. B. Young
Engineering A Change In The Metal-Ion Specificity Of The Iron-Depedent Superoxide Dismutase From Mycobacterium Tuberculosis. X-Ray Structure Analysis Of Site-Directed Mutants.
Eur. J. Biochem. V. 251 795 1998
PubMed-ID: 9490054 | Reference-DOI: 10.1046/J.1432-1327.1998.2510795.X

Molecule 1 - SUPEROXIDE DISMUTASE
	Chains	:	A, B
	EC Number	:	1.15.1.1
	Engineered	:	YES
	Expression System	:	MYCOBACTERIUM VACCAE
	Expression System Taxid	:	1810
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773

		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	FE	2	Ligand/Ion	FE (III) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:28 , HIS A:76 , ASP A:160 , HIS A:164	BINDING SITE FOR RESIDUE FE A1200
2	AC2	SOFTWARE	HIS B:28 , HIS B:76 , ASP B:160 , HIS B:164	BINDING SITE FOR RESIDUE FE B1200

(no "SS Bond" information available for 1GN3)

Asymmetric Unit

No.	Residues
1	Glu A:17	-	Pro A:18
2	Glu B:17	-	Pro B:18

(no "SAP(SNP)/Variant" information available for 1GN3)

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.	SODF_MYCTO	160-167	2	A:160-167 B:160-167
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODF_MYCTU	160-167	2	A:160-167 B:160-167

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODF_MYCTO	160-167	4	A:160-167 B:160-167
1	SOD_MN	PS00088	Manganese and iron superoxide dismutases signature.	SODF_MYCTU	160-167	4	A:160-167 B:160-167

(no "Exon" information available for 1GN3)

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 SODF_MYCTO | P9WGE6 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
           SODF_MYCTO     2 AEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDHQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATS 199
               SCOP domains d1gn3a1 A:2-85 Fe superoxide dismutase (FeSOD)                                      d1gn3a2 A:86-199 Fe superoxide dismutase (FeSOD)                                                                   SCOP domains
               CATH domains -------------------1gn3A01 A:21-84 Fe,Mn superoxide dismutase (SOD) domain         ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.........eeeeeeee.hhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gn3 A   2 AEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDQQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATS 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain A from PDB  Type:PROTEIN  Length:198
 aligned with SODF_MYCTU | P9WGE7 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
           SODF_MYCTU     2 AEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDHQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATS 199
               SCOP domains d1gn3a1 A:2-85 Fe superoxide dismutase (FeSOD)                                      d1gn3a2 A:86-199 Fe superoxide dismutase (FeSOD)                                                                   SCOP domains
               CATH domains -------------------1gn3A01 A:21-84 Fe,Mn superoxide dismutase (SOD) domain         ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.........eeeeeeee.hhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gn3 A   2 AEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDQQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATS 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with SODF_MYCTO | P9WGE6 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
           SODF_MYCTO     2 AEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDHQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATS 199
               SCOP domains d1gn3b1 B:2-85 Fe superoxide dismutase (FeSOD)                                      d1gn3b2 B:86-199 Fe superoxide dismutase (FeSOD)                                                                   SCOP domains
               CATH domains -------------------1gn3B01 B:21-84 Fe,Mn superoxide dismutase (SOD) domain         ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.........eeeeeeee.hhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gn3 B   2 AEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDQQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATS 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with SODF_MYCTU | P9WGE7 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
           SODF_MYCTU     2 AEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDHQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATS 199
               SCOP domains d1gn3b1 B:2-85 Fe superoxide dismutase (FeSOD)                                      d1gn3b2 B:86-199 Fe superoxide dismutase (FeSOD)                                                                   SCOP domains
               CATH domains -------------------1gn3B01 B:21-84 Fe,Mn superoxide dismutase (SOD) domain         ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.........eeeeeeee.hhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gn3 B   2 AEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIADAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDQQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATS 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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 '\|'

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: Fe,Mn superoxide dismutase (SOD) domain (14)

Mycobacterium tuberculosis. Organism_taxid: 1773. (4)

1a	1gn3A01	A:21-84
1b	1gn3B01	B:21-84

(no "Pfam Domain" information available for 1GN3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SODF_MYCTU | P9WGE7)

molecular function
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) 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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004784	superoxide dismutase activity	Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
	GO:0052059	evasion or tolerance by symbiont of host-produced reactive oxygen species	The process in which an organism avoids the effects of reactive oxygen species produced as a defense response by the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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:0006979	response to oxidative stress	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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B (SODF_MYCTO | P9WGE6)

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: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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Glu A:17 - Pro A:18	[ RasMol ]
		Glu B:17 - Pro B:18	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	1gn3
		Family and Domain Information	:	ProDom \| SYSTERS
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	SODF_MYCTO \| P9WGE6
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	SODF_MYCTU \| P9WGE7
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	1.15.1.1
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	SODF_MYCTO \| P9WGE6
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	SODF_MYCTU \| P9WGE7
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UniProtKB/Swiss-Prot
	SODF_MYCTO \| P9WGE6	:	1gn2 1gn4 1gn6 1ids
	SODF_MYCTU \| P9WGE7	:	1gn2 1gn4 1gn6 1ids

1gn2	S123C MUTANT OF THE IRON-SUPEROXIDE DISMUTASE FROM MYCOBACTERIUM TUBERCULOSIS.
1gn4	H145E MUTANT OF THE IRON-SUPEROXIDE DISMUTASE FROM MYCOBACTERIUM TUBERCULOSIS.
1gn6	G152A MUTANT OF THE IRON-SUPEROXIDE DISMUTASE FROM MYCOBACTERIUM TUBERCULOSIS.
1ids	IRON-DEPENDENT SUPEROXIDE DISMUTASE (FE- SUPEROXIDE DISMUTASE, FE-SOD)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (15, 22)

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