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Title :   THE "RHODANESE" FOLD AND CATALYTIC MECHANISM OF 3-MERCAPTOPYRUVATE SULFOTRANSFERASES: CRYSTAL STRUCTURE OF SSEA FROM ESCHERICHIA COLI

Authors :   A. Spallarossa, F. Forlani, A. Carpen, A. Armirotti, S. Pagani, M. Bolognesi, D. Bordo

Date :   30 Oct 03 (Deposition) - 18 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Sulfur-Transferase, Rhodanese, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Spallarossa, F. Forlani, A. Carpen, A. Armirotti, S. Pagani, M. Bolognesi, D. Bordo
The "Rhodanese" Fold And Catalytic Mechanism Of 3-Mercaptopyruvate Sulfurtransferases: Crystal Structure Of Ssea From Escherichia Coli
J. Mol. Biol. V. 335 583 2004
PubMed-ID: 14672665 | Reference-DOI: 10.1016/J.JMB.2003.10.072

Molecule 1 - 3-MERCAPTOPYRUVATE SULFURTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.8.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEN1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	RESIDUES A186-A189 AND B181-B191 ARE NOT INCLUDED IN THE MODEL.
	Synonym	:	SSEA, RHODANESE-LIKE PROTEIN, MST

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CSS	2	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	SO3	1	Ligand/Ion	SULFITE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	SO3	-1	Ligand/Ion	SULFITE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	SO3	1	Ligand/Ion	SULFITE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE B:223	BINDING SITE FOR RESIDUE SO3 B1268

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

(no "Cis Peptide Bond" information available for 1URH)

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

Asymmetric Unit (3, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHODANESE_3	PS50206	Rhodanese domain profile.	THTM_ECOLI	17-135 165-278	4	A:16-134 B:16-134 A:164-268 B:164-268
2	RHODANESE_1	PS00380	Rhodanese signature 1.	THTM_ECOLI	42-53	2	A:41-52 B:41-52
3	RHODANESE_2	PS00683	Rhodanese C-terminal signature.	THTM_ECOLI	259-269	2	A:258-268 B:258-268

Biological Unit 1 (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHODANESE_3	PS50206	Rhodanese domain profile.	THTM_ECOLI	17-135 165-278	2	A:16-134 - A:164-268 -
2	RHODANESE_1	PS00380	Rhodanese signature 1.	THTM_ECOLI	42-53	1	A:41-52 -
3	RHODANESE_2	PS00683	Rhodanese C-terminal signature.	THTM_ECOLI	259-269	1	A:258-268 -

Biological Unit 2 (3, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RHODANESE_3	PS50206	Rhodanese domain profile.	THTM_ECOLI	17-135 165-278	2	- B:16-134 - B:164-268
2	RHODANESE_1	PS00380	Rhodanese signature 1.	THTM_ECOLI	42-53	1	- B:41-52
3	RHODANESE_2	PS00683	Rhodanese C-terminal signature.	THTM_ECOLI	259-269	1	- B:258-268

(no "Exon" information available for 1URH)

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:263
 aligned with THTM_ECOLI | P31142 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:267
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       
           THTM_ECOLI     3 TTWFVGADWLAEHIDDPEIQIIDARMASPGQEDRNVAQEYLNGHIPGAVFFDIEALSDHTSPLPHMLPRPETFAVAMRELGVNQDKHLIVYDEGNLFSAPRAWWMLRTFGVEKVSILGGGLAGWQRDDLLLEEGAVELPEGEFNAAFNPEAVVKVTDVLLASHENTAQIIDARPAARFNAEVDEPRPGLRRGHIPGALNVPWTELVREGELKTTDELDAIFFGRGVSYDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWSEW 269
               SCOP domains d1urha1 A:2-148 3-mercaptopyruvate sulfurtransferase                                                                                               d1urha2 A:149-268 3-mercaptopyruvate     sulfurtransferase                                                               SCOP domains
               CATH domains 1urhA01 A:2-148 Oxidized Rhodanese, domain 1                                                                                                       1urhA02 A:149-268 Oxidized Rhodanese,     domain 1                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhh......eeeee...........hhhhhhhhh.....ee.hhhhhh...........hhhhhhhhhhhh......eeeee......hhhhhhhhhhhh....eeee.hhhhhhhhh....................hhhh..hhhhhhhhhhhh..eeee..hhhhhh.....----.........ee.hhhhh.......hhhhhhhhhhh........eeee.....hhhhhhhhhhhh.....ee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------RHODANESE_3  PDB: A:16-134 UniProt: 17-135                                                                             -----------------------------RHODANESE_3  PDB: A:164-268 UniProt: 165-278                                                              PROSITE (1)
                PROSITE (2) ---------------------------------------RHODANESE_1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RHODANESE_2 PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1urh A   2 TTWFVGADWLAEHIDDPEIQIIDARMASPGQEDRNVAQEYLNGHIPGAVFFDIEALSDHTSPLPHMLPRPETFAVAMRELGVNQDKHLIVYDEGNLFSAPRAWWMLRTFGVEKVSILGGGLAGWQRDDLLLEEGAVELPEGEFNAAFNPEAVVKVTDVLLASHENTAQIIDARPAARFNAEVDE----LRRGHIPGALNVPWTELVREGELKTTDELDAIFFGRGVSYDKPIIVScGSGVTAAVVLLALATLDVPNVKLYDGAWSEW 268
                                    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       
                                                                                                                                                                                                                 185  190                                            237-CSS

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with THTM_ECOLI | P31142 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:267
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       
           THTM_ECOLI     3 TTWFVGADWLAEHIDDPEIQIIDARMASPGQEDRNVAQEYLNGHIPGAVFFDIEALSDHTSPLPHMLPRPETFAVAMRELGVNQDKHLIVYDEGNLFSAPRAWWMLRTFGVEKVSILGGGLAGWQRDDLLLEEGAVELPEGEFNAAFNPEAVVKVTDVLLASHENTAQIIDARPAARFNAEVDEPRPGLRRGHIPGALNVPWTELVREGELKTTDELDAIFFGRGVSYDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWSEW 269
               SCOP domains d1urhb1 B:2-148 3-mercaptopyruvate sulfurtransferase                                                                                               d1urhb2 B:149-268 3-mercaptopyruv          ate sulfurtransferase                                                         SCOP domains
               CATH domains 1urhB01 B:2-148 Oxidized Rhodanese, domain 1                                                                                                       1urhB02 B:149-268 Oxidized Rhodan          ese, domain 1                                                                 CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------Rhodanese-1urhB01 B:156-26          8                                                                             Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------Rhodanese-1urhB02 B:156-26          8                                                                             Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------Rhodanese-1urhB03 B:156-26          8                                                                             Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------Rhodanese-1urhB04 B:156-26          8                                                                             Pfam domains (4)
         Sec.struct. author ...eehhhhhhhh.....eeeee...........hhhhhhhh......ee..hhhhh.............hhhhhhhhhhh.....eeeee......hhhhhhhhhhhh....eeee.hhhhhhhhh....................hhh.eehhhhhhhhhhhh..eeee..hhhhhh.----------.......ee.hhhh.ee..ee.hhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------RHODANESE_3  PDB: B:16-134 UniProt: 17-135                                                                             -----------------------------RHODANESE_3  PDB: B:164-268 UniProt: 165-278                                                              PROSITE (1)
                PROSITE (2) ---------------------------------------RHODANESE_1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RHODANESE_2 PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1urh B   2 TTWFVGADWLAEHIDDPEIQIIDARMASPGQEDRNVAQEYLNGHIPGAVFFDIEALSDHTSPLPHMLPRPETFAVAMRELGVNQDKHLIVYDEGNLFSAPRAWWMLRTFGVEKVSILGGGLAGWQRDDLLLEEGAVELPEGEFNAAFNPEAVVKVTDVLLASHENTAQIIDARPAARFNA----------RGHIPGALNVPWTELVREGELKTTDELDAIFFGRGVSYDKPIIVScGSGVTAAVVLLALATLDVPNVKLYDGAWSEW 268
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         -|      201       211       221       231     | 241       251       261       
                                                                                                                                                                                                             181        192                                          237-CSS

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: Rhodanese/Cell cycle control phosphatase (39)

Superfamily: Rhodanese/Cell cycle control phosphatase (39)

Family: Multidomain sulfurtransferase (rhodanese) (14)

Protein domain: 3-mercaptopyruvate sulfurtransferase (2)

Escherichia coli [TaxId: 562] (1)

1a	d1urha1	A:2-148
1b	d1urha2	A:149-268
1c	d1urhb1	B:2-148
1d	d1urhb2	B:149-268

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Oxidized Rhodanese; domain 1 (42)

Homologous Superfamily: Oxidized Rhodanese, domain 1 (42)

Escherichia coli. Organism_taxid: 562. (1)

1a	1urhA01	A:2-148
1b	1urhB01	B:2-148
1c	1urhA02	A:149-268
1d	1urhB02	B:149-268

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Rhodanese] (33)

Family: Rhodanese (33)

Escherichia coli (strain K12) (6)

1a	Rhodanese-1urhB01	B:156-268
1b	Rhodanese-1urhB02	B:156-268
1c	Rhodanese-1urhB03	B:156-268
1d	Rhodanese-1urhB04	B:156-268

Asymmetric Unit(hide GO term definitions)

Chain A,B (THTM_ECOLI | P31142)

molecular function
	GO:0016784	3-mercaptopyruvate sulfurtransferase activity	Catalysis of the reaction: 3-mercaptopyruvate + cyanide = pyruvate + thiocyanate.
	GO:0004792	thiosulfate sulfurtransferase activity	Catalysis of the reaction: hydrogen cyanide + thiosulfate = H(+) + sulfite + thiocyanate.
	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:0046677	response to antibiotic	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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
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.

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