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Biological Unit 2 (Jmol Viewer)

Title :   SYNCHROTRON REDUCED FORM OF THE N-TERMINAL DOMAIN OF SALMONELLA TYPHIMURIUM AHPF

Authors :   B. R. Roberts, Z. A. Wood, T. J. Jonsson, L. B. Poole, P. A. Karplus

Date :   10 Jun 05 (Deposition) - 21 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Thioredoxin, Disulfide, Peroxiredoxin, Thiolate, Alkyl Hydroperoxide Reductase, Synchrotron Radiation, Pka, Radiation Damage, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. R. Roberts, Z. A. Wood, T. J. Jonsson, L. B. Poole, P. A. Karplus
Oxidized And Synchrotron Cleaved Structures Of The Disulfide Redox Center In The N-Terminal Domain Of Salmonella Typhimurium Ahpf
Protein Sci. V. 14 2414 2005
PubMed-ID: 16131664 | Reference-DOI: 10.1110/PS.051459705
(for further references see the PDB file header)

Molecule 1 - ALKYL HYDROPEROXIDE REDUCTASE SUBUNIT F
	Chains	:	A, B
	EC Number	:	1.6.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-202
	Gene	:	AHPF
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Synonym	:	ALKYL HYDROPEROXIDE REDUCTASE F52A PROTEIN

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ZYP)

(no "Site" information available for 1ZYP)

Asymmetric Unit

No.	Residues
1	A:129	-	A:132
2	B:129	-	B:132

Asymmetric Unit

No.	Residues
1	Lys A:62	-	Pro A:63
2	Val A:171	-	Pro A:172
3	Lys B:62	-	Pro B:63
4	Val B:171	-	Pro B:172

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTAREDOXIN_2	PS51354	Glutaredoxin domain profile.	AHPF_SALTY	109-208	2	A:109-196 B:109-196

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTAREDOXIN_2	PS51354	Glutaredoxin domain profile.	AHPF_SALTY	109-208	1	A:109-196 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTAREDOXIN_2	PS51354	Glutaredoxin domain profile.	AHPF_SALTY	109-208	1	- B:109-196

(no "Exon" information available for 1ZYP)

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 AHPF_SALTY | P19480 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      
           AHPF_SALTY     1 MLDTNMKTQLRAYLEKLTKPVELIATLDDSAKSAEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNPGSQQGPRFAGSPLGHEFTSLVLALLWTGGHPSKEAQSLLEQIRDIDGDFEFETYYSLSCHNCPDVVQALNLMAVLNPRIKHTAIDGGTFQNEITERNVMGVPAVFVNGKEFGQGRMTLTEIVAKVD 196
               SCOP domains d1zypa1 A:1-102 Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain                     d1zypa2 A:103-196 Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhh....eeeee.........eeeee........eee...hhhhhhhhhhhhhhhh......hhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeee..eeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------GLUTAREDOXIN_2  PDB: A:109-196 UniProt: 109-208                                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zyp A   1 MLDTNMKTQLRAYLEKLTKPVELIATLDDSAKSAEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNPGSQQGPRFAGSPLGHEFTSLVLALLWTGGHPSKEAQSLLEQIRDIDGDFEFETYYSLSCHNCPDVVQALNLMAVLNPRIKHTAIDGGTFQNEITERNVMGVPAVFVNGKEFGQGRMTLTEIVAKVD 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 AHPF_SALTY | P19480 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      
           AHPF_SALTY     1 MLDTNMKTQLRAYLEKLTKPVELIATLDDSAKSAEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNPGSQQGPRFAGSPLGHEFTSLVLALLWTGGHPSKEAQSLLEQIRDIDGDFEFETYYSLSCHNCPDVVQALNLMAVLNPRIKHTAIDGGTFQNEITERNVMGVPAVFVNGKEFGQGRMTLTEIVAKVD 196
               SCOP domains d1zypb1 B:1-102 Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain                     d1zypb2 B:103-196 Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------Thioredoxin_3-1zypB01 B:119-196                                                Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------Thioredoxin_3-1zypB02 B:119-196                                                Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhh....eeeee.........eeeee........eee...hhhhhhhhhhhhhhhh......hhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh......eeee..eeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------GLUTAREDOXIN_2  PDB: B:109-196 UniProt: 109-208                                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zyp B   1 MLDTNMKTQLRAYLEKLTKPVELIATLDDSAKSAEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNPGSQQGPRFAGSPLGHEFTSLVLALLWTGGHPSKEAQSLLEQIRDIDGDFEFETYYSLSCHNCPDVVQALNLMAVLNPRIKHTAIDGGTFQNEITERNVMGVPAVFVNGKEFGQGRMTLTEIVAKVD 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 '\|'

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: PDI-like (13)

Protein domain: Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain (3)

Salmonella typhimurium [TaxId: 90371] (3)

1a	d1zypa1	A:1-102
1b	d1zypa2	A:103-196
1c	d1zypb1	B:1-102
1d	d1zypb2	B:103-196

(no "CATH Domain" information available for 1ZYP)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: Thioredoxin_3 (4)

Salmonella typhimurium (2)

1a	Thioredoxin_3-1zypB01	B:119-196
1b	Thioredoxin_3-1zypB02	B:119-196

Asymmetric Unit(hide GO term definitions)

Chain A,B (AHPF_SALTY | P19480)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0008785	alkyl hydroperoxide reductase activity	Catalysis of the reaction: octane hydroperoxide + NADH + H+ = H2O + NAD+ + 1-octanol.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	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:0016651	oxidoreductase activity, acting on NAD(P)H	Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	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: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.
cellular component
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Lys A:62 - Pro A:63	[ RasMol ]
		Lys B:62 - Pro B:63	[ RasMol ]
		Val A:171 - Pro A:172	[ RasMol ]
		Val B:171 - Pro B:172	[ RasMol ]

Biological Units
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	1zyp
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	AHPF_SALTY \| P19480
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	1.6.4.-
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UniProtKB/Swiss-Prot
	AHPF_SALTY \| P19480	:	1hyu 1zyn

1hyu	STRUCTURE OF THE INTACT AHPF PROTEIN
1zyn	OXIDIZED FORM OF THE NTD DOMAIN OF AHPF

Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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