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Title :   CRYSTAL STRUCTURE AT 1.25 ANGSTROMS RESOLUTION OF THE CYS55SER VARIANT OF THE THIOREDOXIN-LIKE [2FE-2S] FERREDOXIN FROM AQUIFEX AEOLICUS

Authors :   A. P. Yeh, X. I. Ambroggio, S. L. A. Andrade, O. Einsle, C. Chatelet, J. Meyer, D. C. Rees

Date :   22 Jun 02 (Deposition) - 18 Sep 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ferredoxin, Thioredoxin-Like Fold, [2Fe-2S] Cluster, Cys55Ser Variant, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Yeh, X. I. Ambroggio, S. L. A. Andrade, O. Einsle, C. Chatelet, J. Meyer, D. C. Rees
High-Resolution Crystal Structures Of The Wild Type And Cys-55-->Ser And Cys-59-->Ser Variants Of The Thioredoxin-Like [2Fe-2S] Ferredoxin From Aquifex Aeolicus
J. Biol. Chem. V. 277 34499 2002
PubMed-ID: 12089152 | Reference-DOI: 10.1074/JBC.M205096200
(for further references see the PDB file header)

Molecule 1 - [2FE-2S] FERREDOXIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	K38
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FDX4
	Mutation	:	YES
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:9 , GLN A:11 , CYS A:22 , SER A:55 , MET A:56 , ALA A:58 , CYS A:59	BINDING SITE FOR RESIDUE FES A 301
2	AC2	SOFTWARE	CYS B:9 , GLN B:11 , CYS B:22 , SER B:55 , MET B:56 , ALA B:58 , CYS B:59	BINDING SITE FOR RESIDUE FES B 301

(no "SS Bond" information available for 1M2B)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:62	-	Pro A:63
2	Tyr A:68	-	Pro A:69
3	Gly B:62	-	Pro B:63
4	Tyr B:68	-	Pro B:69

(no "SAP(SNP)/Variant" information available for 1M2B)

(no "PROSITE Motif" information available for 1M2B)

(no "Exon" information available for 1M2B)

Asymmetric/Biological 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:101
 aligned with FER2_AQUAE | O66511 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:101
                                    13        23        33        43        53        63        73        83        93       103 
           FER2_AQUAE     4 FKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGCMNACMMGPVVVVYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERLVISK 104
               SCOP domains d1m2ba_ A: Thioredoxin-like 2Fe-2S ferredoxin                                                         SCOP domains
               CATH domains 1m2bA00 A:3-103 Glutaredoxin                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee................hhhhhhhhhhhhhh.hhhhhh.eeeeee....hhhhh..eeee...eee...hhhhhhhhhhhh......hhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1m2b A   3 FKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGSMNACMMGPVVVVYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERLVISK 103
                                    12        22        32        42        52        62        72        82        92       102

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with FER2_AQUAE | O66511 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:101
                                    13        23        33        43        53        63        73        83        93       103 
           FER2_AQUAE     4 FKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGCMNACMMGPVVVVYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERLVISK 104
               SCOP domains d1m2bb_ B: Thioredoxin-like 2Fe-2S ferredoxin                                                         SCOP domains
               CATH domains 1m2bB00 B:3-103 Glutaredoxin                                                                          CATH domains
           Pfam domains (1) ---------------Complex1_24kDa-1m2bB01 B:18-90                                           ------------- Pfam domains (1)
           Pfam domains (2) ---------------Complex1_24kDa-1m2bB02 B:18-90                                           ------------- Pfam domains (2)
         Sec.struct. author .eeeeee............hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhh..eeee...eee...hhhhhhhhhhhh......hhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1m2b B   3 FKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGSMNACMMGPVVVVYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERLVISK 103
                                    12        22        32        42        52        62        72        82        92       102

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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/Biological 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: Thioredoxin-like 2Fe-2S ferredoxin (4)

Protein domain: Thioredoxin-like 2Fe-2S ferredoxin (4)

Aquifex aeolicus [TaxId: 63363] (4)

1a	d1m2ba_	A:
1b	d1m2bb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Aquifex aeolicus. Organism_taxid: 63363. (3)

1a	1m2bA00	A:3-103
1b	1m2bB00	B:3-103

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Complex1_24kDa] (3)

Family: Complex1_24kDa (3)

Aquifex aeolicus (2)

1a	Complex1_24kDa-1m2bB01	B:18-90
1b	Complex1_24kDa-1m2bB02	B:18-90

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FER2_AQUAE | O66511)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	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:0003954	NADH dehydrogenase activity	Catalysis of the reaction: NADH + H+ + acceptor = NAD+ + reduced acceptor.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009060	aerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:62 - Pro A:63	[ RasMol ]
		Gly B:62 - Pro B:63	[ RasMol ]
		Tyr A:68 - Pro A:69	[ RasMol ]
		Tyr B:68 - Pro B:69	[ RasMol ]

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	1m2b
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	FER2_AQUAE \| O66511	:	1f37 1m2a 1m2d

1f37	STRUCTURE AT 2.3 ANGSTROMS RESOLUTION OF WILD TYPE AQUIFEX AEOLICUS [2FE-2S] FERREDOXIN
1m2a	STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF WILD TYPE AQUIFEX AEOLICUS [2FE-2S] FERREDOXIN
1m2d	STRUCTURE AT 1.05 ANGSTROMS RESOLUTION OF THE CYS59SER VARIANT OF AQUIFEX AEOLICUS [2FE-2S] FERREDOXIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (9, 9)

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