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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF SUFC-SUFD COMPLEX INVOLVED IN THE IRON-SULFUR CLUSTER BIOSYNTHESIS

Authors :   K. Wada

Date :   11 Oct 08 (Deposition) - 10 Mar 09 (Release) - 21 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Iron-Sulfur Cluster, Abc-Atpase, Atp-Binding, Cytoplasm, Nucleotide-Binding, Transport, Biosynthetic Protein/Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Wada, N. Sumi, R. Nagai, K. Iwasaki, T. Sato, K. Suzuki, Y. Hasegawa, S. Kitaoka, Y. Minami, F. W. Outten, Y. Takahashi, K. Fukuyama
Molecular Dynamism Of Fe-S Cluster Biosynthesis Implicated By The Structure Of Sufc(2)-Sufd(2) Complex
J. Mol. Biol. V. 387 245 2009
PubMed-ID: 19361433 | Reference-DOI: 10.1016/J.JMB.2009.01.054
(for further references see the PDB file header)

Molecule 1 - PROTEIN SUFD
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMW219
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SUFC AND SUFD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

Molecule 2 - PROBABLE ATP-DEPENDENT TRANSPORTER SUFC
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMW219
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SUFC AND SUFD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE C:16 , GLY C:37 , GLY C:39 , LYS C:40 , SER C:41 , THR C:42 , HOH C:2038	BINDING SITE FOR RESIDUE MES C 2000

(no "SS Bond" information available for 2ZU0)

(no "Cis Peptide Bond" information available for 2ZU0)

(no "SAP(SNP)/Variant" information available for 2ZU0)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	SUFC_ECOLI	146-160	2	C:146-160 D:155-160

(no "Exon" information available for 2ZU0)

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:416
 aligned with SUFD_ECOLI | P77689 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:416
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417      
           SUFD_ECOLI     8 SNALQQWHHLFEAEGTKRSPQAQQHLQQLLRTGLPTRKHENWKYTPLEGLINSQFVSIAGEISPQQRDALALTLDSVRLVFVDGRYVPALSDATEGSGYEVSINDDRQGLPDAIQAEVFLHLTESLAQSVTHIAVKRGQRPAKPLLLMHITQGVAGEEVNTAHYRHHLDLAEGAEATVIEHFVSLNDARHFTGARFTINVAANAHLQHIKLAFENPLSHHFAHNDLLLAEDATAFSHSFLLGGAVLRHNTSTQLNGENSTLRINSLAMPVKNEVCDTRTWLEHNKGFCNSRQLHKTIVSDKGRAVFNGLINVAQHAIKTDGQMTNNNLLMGKLAEVDTKPQLEIYADDVKCSHGATVGRIDDEQIFYLRSRGINQQDAQQMIIYAFAAELTEALRDEGLKQQVLARIGQRLPGGAR 423
               SCOP domains d2zu0a_ A: Stabilizer of iron transporter SufD                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.............hhhhhh..ee......hhhhhhhhh.....eeeeee..ee.hhhh........eeeee............hhhhhhhhhhh..eeeeee.........eeeeeee.......eeeeeeeeeeee....eeeeeeeeee.....eeeeeeeeeee....eeeeeeeee.....eeeeeeeeee....eeeeeeee....eeeeeeeeee.....eeeeeeee......eeeeeeeeee.....eeeeeeeeee....eeeeeeeeee......eeeeeeeeeee.....eeeeeeeeee....eeeeeeeeeee.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zu0 A   8 SNALQQWHHLFEAEGTKRSPQAQQHLQQLLRTGLPTRKHENWKYTPLEGLINSQFVSIAGEISPQQRDALALTLDSVRLVFVDGRYVPALSDATEGSGYEVSINDDRQGLPDAIQAEVFLHLTESLAQSVTHIAVKRGQRPAKPLLLMHITQGVAGEEVNTAHYRHHLDLAEGAEATVIEHFVSLNDARHFTGARFTINVAANAHLQHIKLAFENPLSHHFAHNDLLLAEDATAFSHSFLLGGAVLRHNTSTQLNGENSTLRINSLAMPVKNEVCDTRTWLEHNKGFCNSRQLHKTIVSDKGRAVFNGLINVAQHAIKTDGQMTNNNLLMGKLAEVDTKPQLEIYADDVKCSHGATVGRIDDEQIFYLRSRGINQQDAQQMIIYAFAAELTEALRDEGLKQQVLARIGQRLPGGAR 423
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417

Chain B from PDB  Type:PROTEIN  Length:414
 aligned with SUFD_ECOLI | P77689 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:414
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418    
           SUFD_ECOLI     9 NALQQWHHLFEAEGTKRSPQAQQHLQQLLRTGLPTRKHENWKYTPLEGLINSQFVSIAGEISPQQRDALALTLDSVRLVFVDGRYVPALSDATEGSGYEVSINDDRQGLPDAIQAEVFLHLTESLAQSVTHIAVKRGQRPAKPLLLMHITQGVAGEEVNTAHYRHHLDLAEGAEATVIEHFVSLNDARHFTGARFTINVAANAHLQHIKLAFENPLSHHFAHNDLLLAEDATAFSHSFLLGGAVLRHNTSTQLNGENSTLRINSLAMPVKNEVCDTRTWLEHNKGFCNSRQLHKTIVSDKGRAVFNGLINVAQHAIKTDGQMTNNNLLMGKLAEVDTKPQLEIYADDVKCSHGATVGRIDDEQIFYLRSRGINQQDAQQMIIYAFAAELTEALRDEGLKQQVLARIGQRLPGGA 422
               SCOP domains d2zu0b_ B: Stabilizer of iron transporter SufD                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------UPF0051-2zu0B01 B:164-393                                                                                                                                                                                                             ----------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------UPF0051-2zu0B02 B:164-393                                                                                                                                                                                                             ----------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhh..ee......hhhhhhhhh.....eeeeee..ee.hhhh........eeeee............hhhhhhhhhhh..eeeeee.........eeeeeee.......eeeeeeeeeeee....eeeeeeeeee.....eeeeeeeeeee....eeeeeeeee.....eeeeeeeeee....eeeeeeee....eeeeeeeeee.....eeeeeeee......eeeeeeeeee.....eeeeeeeeee....eeeeeeeeee.......eeeeeeeeee.....eeeeeeeeee.....eeeeeeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zu0 B   9 NALQQWHHLFEAEGTKRSPQAQQHLQQLLRTGLPTRKHENWKYTPLEGLINSQFVSIAGEISPQQRDALALTLDSVRLVFVDGRYVPALSDATEGSGYEVSINDDRQGLPDAIQAEVFLHLTESLAQSVTHIAVKRGQRPAKPLLLMHITQGVAGEEVNTAHYRHHLDLAEGAEATVIEHFVSLNDARHFTGARFTINVAANAHLQHIKLAFENPLSHHFAHNDLLLAEDATAFSHSFLLGGAVLRHNTSTQLNGENSTLRINSLAMPVKNEVCDTRTWLEHNKGFCNSRQLHKTIVSDKGRAVFNGLINVAQHAIKTDGQMTNNNLLMGKLAEVDTKPQLEIYADDVKCSHGATVGRIDDEQIFYLRSRGINQQDAQQMIIYAFAAELTEALRDEGLKQQVLARIGQRLPGGA 422
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418

Chain C from PDB  Type:PROTEIN  Length:247
 aligned with SUFC_ECOLI | P77499 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           SUFC_ECOLI     1 MLSIKDLHVSVEDKAILRGLSLDVHPGEVHAIMGPNGSGKSTLSATLAGREDYEVTGGTVEFKGKDLLALSPEDRAGEGIFMAFQYPVEIPGVSNQFFLQTALNAVRSYRGQETLDRFDFQDLMEEKIALLKMPEDLLTRSVNVGFSGGEKKRNDILQMAVLEPELCILDESDSGLDIDALKVVADGVNSLRDGKRSFIIVTHYQRILDYIKPDYVHVLYQGRIVKSGDFTLVKQLEEQGYGWLTEQ 247
               SCOP domains d2zu0c_ C: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeeeeeee....eeeee.....hhhhhhhhhhh....eeeeeeeee..ee.hhhhhhhhhhhheeee..........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhh......eeeee..hhhhhhh....eeeeee..eeeeee..hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zu0 C   1 MLSIKDLHVSVEDKAILRGLSLDVHPGEVHAIMGPNGSGKSTLSATLAGREDYEVTGGTVEFKGKDLLALSPEDRAGEGIFMAFQYPVEIPGVSNQFFLQTALNAVRSYRGQETLDRFDFQDLMEEKIALLKMPEDLLTRSVNVGFSGGEKKRNDILQMAVLEPELCILDESDSGLDIDALKVVADGVNSLRDGKRSFIIVTHYQRILDYIKPDYVHVLYQGRIVKSGDFTLVKQLEEQGYGWLTEQ 247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain D from PDB  Type:PROTEIN  Length:42
 aligned with SUFC_ECOLI | P77499 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:108
                                    95       105       115       125       135       145       155       165       175       185        
           SUFC_ECOLI    86 YPVEIPGVSNQFFLQTALNAVRSYRGQETLDRFDFQDLMEEKIALLKMPEDLLTRSVNVGFSGGEKKRNDILQMAVLEPELCILDESDSGLDIDALKVVADGVNSLRD 193
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ABC_tran-2zu0D01 D:86                                                -164                        ----------- Pfam domains (1)
           Pfam domains (2) ABC_tran-2zu0D02 D:86                                                -164                        ----------- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhh------------------------------------------------hhhhhhhhh.------------------hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ABC_TRANSPORTER--------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2zu0 D  86 YPVEIPGVSNQFFLQTALNAV------------------------------------------------DILQMAVLEP------------------VVADGVNSLRD 193
                                    95       105|        -         -         -         -       155        |-         -       185        
                                              106                                              155      164                183

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 2ZU0)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: ABC_tran (53)

Escherichia coli (strain K12) (10)

1a	ABC_tran-2zu0D01	D:86-164
1b	ABC_tran-2zu0D02	D:86-164

Clan: no clan defined [family: UPF0051] (2)

Family: UPF0051 (2)

Escherichia coli (strain K12) (2)

2a	UPF0051-2zu0B01	B:164-393
2b	UPF0051-2zu0B02	B:164-393

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SUFD_ECOLI | P77689)

molecular function
	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:0016226	iron-sulfur cluster assembly	The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
	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.

Chain C,D (SUFC_ECOLI | P77499)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0016226	iron-sulfur cluster assembly	The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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