1P3W - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   X-RAY CRYSTAL STRUCTURE OF E. COLI ISCS

Authors :   J. R. Cupp-Vickery, L. E. Vickery, H. Urbina

Date :   18 Apr 03 (Deposition) - 22 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Iron Sulfur Cluster, Nifs, Csdb, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Cupp-Vickery, H. Urbina, L. E. Vickery
Crystal Structure Of Iscs, A Cysteine Desulfurase From Escherichia Coli
J. Mol. Biol. V. 330 1049 2003
PubMed-ID: 12860127 | Reference-DOI: 10.1016/S0022-2836(03)00690-9

Molecule 1 - CYSTEINE DESULFURASE
	Chains	:	B, A
	EC Number	:	4.4.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ISCS OR B2530 OR C3056 OR Z3797 OR ECS3396 OR SF2577
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	THII TRANSPERSULFIDASE, NIFS PROTEIN HOMOLOG

		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	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:243 , HOH A:880 , ALA B:75 , THR B:76 , HIS B:104 , MET B:151 , ASN B:155 , ASP B:180 , THR B:182 , GLN B:183 , SER B:203 , HIS B:205 , LYS B:206 , HOH B:795 , HOH B:848 , HOH B:925	BINDING SITE FOR RESIDUE PLP B 764
2	AC2	SOFTWARE	ALA A:75 , THR A:76 , HIS A:104 , MET A:151 , ASN A:155 , ASP A:180 , THR A:182 , GLN A:183 , SER A:203 , HIS A:205 , LYS A:206 , HOH A:801 , HOH A:823 , HOH A:895 , THR B:243	BINDING SITE FOR RESIDUE PLP A 764

(no "SS Bond" information available for 1P3W)

Asymmetric/Biological Unit

No.	Residues
1	Lys B:221	-	Pro B:222
2	Lys A:221	-	Pro A:222

(no "SAP(SNP)/Variant" information available for 1P3W)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_5	PS00595	Aminotransferases class-V pyridoxal-phosphate attachment site.	ISCS_ECOLI	197-216	2	A:197-216 B:197-216

(no "Exon" information available for 1P3W)

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:385
 aligned with ISCS_ECOLI | P0A6B7 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           ISCS_ECOLI     2 KLPIYLDYSATTPVDPRVAEKMMQFMTMDGTFGNPASRSHRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNLAIKGAANFYQKKGKHIITSKTEHKAVLDTCRQLEREGFEVTYLAPQRNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGEMCRARGIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGPKGIGALYVRRKPRVRIEAQMHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEEVYLNGDLEHGAPNILNVSFNYVEGESLIMALKDLAVSSGSACTSASLEPSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRDLSPLWEMYKQ 392
               SCOP domains d1p3wa_ A: Cysteine desulfurase IscS                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -1p3wA01      1p3wA02 A:16-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   1p3wA01 A:3-15,A:263-376 Aspartate Aminotransferase, domain 1                                                     ---------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.........hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee.hhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhh..eeeee........hhhhhhhhh...eeeee............hhhhhhhhhhhh..eeeee..................eeeee..........eeeee..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee..........eeeeee...hhhhhhhhh..ee......------..hhhhhhhh.hhhhhhheeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p3w A   2 KLPIYLDYSATTPVDPRVAEKMMQFMTMDGTFGNPASRSHRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNLAIKGAANFYQKKGKHIITSKTEHKAVLDTCRQLEREGFEVTYLAPQRNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGEMCRARGIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGPKGIGALYVRRKPRVRIEAQMHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEEVYLNGDLEHGAPNILNVSFNYVEGESLIMALKDLAVSSGSA------EPSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRDLSPLWEMYKQ 392
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321     |   -  |    341       351       361       371       381       391 
                                                                                                                                                                                                                                                                                                                                                               327    334

Chain B from PDB  Type:PROTEIN  Length:385
 aligned with ISCS_ECOLI | P0A6B7 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           ISCS_ECOLI     2 KLPIYLDYSATTPVDPRVAEKMMQFMTMDGTFGNPASRSHRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNLAIKGAANFYQKKGKHIITSKTEHKAVLDTCRQLEREGFEVTYLAPQRNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGEMCRARGIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGPKGIGALYVRRKPRVRIEAQMHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEEVYLNGDLEHGAPNILNVSFNYVEGESLIMALKDLAVSSGSACTSASLEPSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRDLSPLWEMYKQ 392
               SCOP domains d1p3wb_ B: Cysteine desulfurase IscS                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -1p3wB01      1p3wB02 B:16-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   1p3wB01 B:3-15,B:263-376 Aspartate Aminotransferase, domain 1                                                     ---------------- CATH domains
           Pfam domains (1) ---Aminotran_5-1p3wB01 B:5-369                                                                                                                                                                                                                                                                                                                                                  ----------------------- Pfam domains (1)
           Pfam domains (2) ---Aminotran_5-1p3wB02 B:5-369                                                                                                                                                                                                                                                                                                                                                  ----------------------- Pfam domains (2)
         Sec.struct. author ...ee.........hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee.hhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhh..eeeee........hhhhhhhhh...eeeee............hhhhhhhhhhhhh.eeeee..................eeeee..........eeeee..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.........eeeeee...hhhhhhhhh..ee......------..hhhhhhhh.hhhhhhheeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p3w B   2 KLPIYLDYSATTPVDPRVAEKMMQFMTMDGTFGNPASRSHRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNLAIKGAANFYQKKGKHIITSKTEHKAVLDTCRQLEREGFEVTYLAPQRNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGEMCRARGIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGPKGIGALYVRRKPRVRIEAQMHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEEVYLNGDLEHGAPNILNVSFNYVEGESLIMALKDLAVSSGSA------EPSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRDLSPLWEMYKQ 392
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321     |   -  |    341       351       361       371       381       391 
                                                                                                                                                                                                                                                                                                                                                               327    334

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: Cystathionine synthase-like (64)

Protein domain: Cysteine desulfurase IscS (1)

Escherichia coli [TaxId: 562] (1)

1a	d1p3wa_	A:
1b	d1p3wb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Aspartate Aminotransferase; domain 2 (384)

Homologous Superfamily: Type I PLP-dependent aspartate aminotransferase-like (Major domain) (384)

Escherichia coli. Organism_taxid: 562. (37)

1a	1p3wA02	A:16-262
1b	1p3wB02	B:16-262

Architecture: Alpha-Beta Complex (3881)

Topology: Aspartate Aminotransferase, domain 1 (355)

Homologous Superfamily: Aspartate Aminotransferase, domain 1 (354)

Escherichia coli. Organism_taxid: 562. (32)

2a	1p3wA01	A:3-15,A:263-376
2b	1p3wB01	B:3-15,B:263-376

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: Aminotran_5 (20)

Escherichia coli (strain K12) (3)

1a	Aminotran_5-1p3wB01	B:5-369
1b	Aminotran_5-1p3wB02	B:5-369

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ISCS_ECOLI | P0A6B7)

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:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0031071	cysteine desulfurase activity	Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine.
	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.
	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:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	GO:0009000	selenocysteine lyase activity	Catalysis of the reaction: L-selenocysteine + reduced acceptor = hydrogen selenide + L-alanine + acceptor.
	GO:0097163	sulfur carrier activity	Enables the directed movement of sulfur into, out of or within a cell, or between cells.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0044571	[2Fe-2S] cluster assembly	The incorporation of two iron atoms and two sulfur atoms into an iron-sulfur cluster.
	GO:0016226	iron-sulfur cluster assembly	The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
	GO:0018131	oxazole or thiazole biosynthetic process	The chemical reactions and pathways resulting in the formation of oxazole or thiazole, five-membered heterocyclic ring structures containing an oxygen and a sulfur, respectively, in the 1-position and a nitrogen in the 3-position.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	GO:0031119	tRNA pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.
	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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Ligands, Modified Residues, Ions (1, 2)

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