2BMX - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   MYCOBACTERIUM TUBERCULOSIS AHPC

Authors :   B. G. Guimaraes, P. M. Alzari

Date :   16 Mar 05 (Deposition) - 10 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B  (6x)
Biol. Unit 2: C  (12x)

Keywords :   Peroxiredoxin, Antioxidant Defense System, Mycobacterium Tuberculosis, Oxidoreductase, Structural Proteomics In Europe, Spine, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. G. Guimaraes, H. Souchon, N. Honore, B. Saint-Joanis, R. Brosch, W. Shepard, S. T. Cole, P. M. Alzari
Structure And Mechanism Of The Alkyl Hydroperoxidase Ahpc, A Key Element Of The Mycobacterium Tuberculosis Defense System Against Oxidative Stress.
J. Biol. Chem. V. 280 25735 2005
PubMed-ID: 15886207 | Reference-DOI: 10.1074/JBC.M503076200

Molecule 1 - ALKYL HYDROPEROXIDASE C
	Chains	:	A, B, C
	EC Number	:	1.11.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	ALKYL HYDROPEROXIDE REDUCTASE C, PROTEIN AHPC

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (6x)	:	A	B
Biological Unit 2 (12x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2BMX)

Asymmetric Unit

No.	Residues
1	A:61	-	B:174

(no "Cis Peptide Bond" information available for 2BMX)

(no "SAP(SNP)/Variant" information available for 2BMX)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	AHPC_MYCTO	4-170	3	A:4-170 B:4-170 C:4-170
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	AHPC_MYCTU	4-170	3	A:4-170 B:4-170 C:4-170

Biological Unit 1 (1, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	AHPC_MYCTO	4-170	12	A:4-170 B:4-170 -
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	AHPC_MYCTU	4-170	12	A:4-170 B:4-170 -

Biological Unit 2 (1, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	AHPC_MYCTO	4-170	12	- - C:4-170
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	AHPC_MYCTU	4-170	12	- - C:4-170

(no "Exon" information available for 2BMX)

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:169
 aligned with AHPC_MYCTO | P9WQB6 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           AHPC_MYCTO     2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPMLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQS 170
               SCOP domains d2bmxa1 A:2-170 Alkyl hydroperoxide reductase AhpC                                                                                                                        SCOP domains
               CATH domains 2bmxA00 A:2-170 Glutaredoxin                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhh...hhhh.eeeee.......eeeeee........hhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.hhhhh...eee...hhhhhhh..........eeeeee.....eeeeeee......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --THIOREDOXIN_2  PDB: A:4-170 UniProt: 4-170                                                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmx A   2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPmLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQS 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
                                                                                                                                      110-MSE

Chain A from PDB  Type:PROTEIN  Length:169
 aligned with AHPC_MYCTU | P9WQB7 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           AHPC_MYCTU     2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPMLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQS 170
               SCOP domains d2bmxa1 A:2-170 Alkyl hydroperoxide reductase AhpC                                                                                                                        SCOP domains
               CATH domains 2bmxA00 A:2-170 Glutaredoxin                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhh...hhhh.eeeee.......eeeeee........hhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.hhhhh...eee...hhhhhhh..........eeeeee.....eeeeeee......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --THIOREDOXIN_2  PDB: A:4-170 UniProt: 4-170                                                                                                                              PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmx A   2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPmLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQS 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
                                                                                                                                      110-MSE

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with AHPC_MYCTO | P9WQB6 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
           AHPC_MYCTO     2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPMLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQSDELCACNWR 179
               SCOP domains d2bmxb_ B: Alkyl hydroperoxide reductase AhpC                                                                                                                                      SCOP domains
               CATH domains ------2bmxB01 B:8-179 Glutaredoxin                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...........hhhh.eeeee.......eeeeee........hhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh.....eee...hhhhhhh..........eeeeee.....eeeeeee......hhhhhhhhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --THIOREDOXIN_2  PDB: B:4-170 UniProt: 4-170                                                                                                                             --------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmx B   2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPmLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQSDELCASNWR 179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
                                                                                                                                      110-MSE

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with AHPC_MYCTU | P9WQB7 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
           AHPC_MYCTU     2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPMLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQSDELCACNWR 179
               SCOP domains d2bmxb_ B: Alkyl hydroperoxide reductase AhpC                                                                                                                                      SCOP domains
               CATH domains ------2bmxB01 B:8-179 Glutaredoxin                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...........hhhh.eeeee.......eeeeee........hhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh.....eee...hhhhhhh..........eeeeee.....eeeeeee......hhhhhhhhhhhhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --THIOREDOXIN_2  PDB: B:4-170 UniProt: 4-170                                                                                                                             --------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmx B   2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPmLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQSDELCASNWR 179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
                                                                                                                                      110-MSE

Chain C from PDB  Type:PROTEIN  Length:169
 aligned with AHPC_MYCTO | P9WQB6 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           AHPC_MYCTO     2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPMLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQS 170
               SCOP domains d2bmxc_ C: Alkyl hydroperoxide reductase AhpC                                                                                                                             SCOP domains
               CATH domains 2bmxC00 C:2-170 Glutaredoxin                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhh...hhhh.eeeee.......eeeeee........hhhhhhhhh.hhhhhhh..eeeeeee..hhhhhhhhhhhh.........eee...hhhhhhh..........eeeeee.....eeeeeee......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --THIOREDOXIN_2  PDB: C:4-170 UniProt: 4-170                                                                                                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmx C   2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPmLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQS 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
                                                                                                                                      110-MSE

Chain C from PDB  Type:PROTEIN  Length:169
 aligned with AHPC_MYCTU | P9WQB7 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           AHPC_MYCTU     2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPMLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQS 170
               SCOP domains d2bmxc_ C: Alkyl hydroperoxide reductase AhpC                                                                                                                             SCOP domains
               CATH domains 2bmxC00 C:2-170 Glutaredoxin                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhh...hhhh.eeeee.......eeeeee........hhhhhhhhh.hhhhhhh..eeeeeee..hhhhhhhhhhhh.........eee...hhhhhhh..........eeeeee.....eeeeeee......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --THIOREDOXIN_2  PDB: C:4-170 UniProt: 4-170                                                                                                                              PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmx C   2 PLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPmLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQS 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
                                                                                                                                      110-MSE

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Glutathione peroxidase-like (136)

Protein domain: Alkyl hydroperoxide reductase AhpC (9)

Mycobacterium tuberculosis [TaxId: 1773] (1)

1a	d2bmxa1	A:2-170
1b	d2bmxb_	B:
1c	d2bmxc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. (1)

1a	2bmxA00	A:2-170
1b	2bmxC00	C:2-170
1c	2bmxB01	B:8-179

(no "Pfam Domain" information available for 2BMX)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (AHPC_MYCTU | P9WQB7)

molecular function
	GO:0008785	alkyl hydroperoxide reductase activity	Catalysis of the reaction: octane hydroperoxide + NADH + H+ = H2O + NAD+ + 1-octanol.
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0032843	hydroperoxide reductase activity	Catalysis of the reaction: 2 RSH + ROOH = RSSR + ROH + H2O. This reaction is the thiol-dependent conversion of an organic hydroperoxide to the corresponding alcohol.
	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:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
	GO:0051920	peroxiredoxin activity	Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
	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).
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0052060	evasion or tolerance by symbiont of host-produced nitric oxide	The process in which an organism avoids the effects of nitric oxide 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: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:0051409	response to nitrosative 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 a nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	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: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,C (AHPC_MYCTO | P9WQB6)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	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:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
	GO:0051920	peroxiredoxin activity	Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	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.

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