2Q3D - JenaLib

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Title :   2.2 A RESOLUTION CRYSTAL STRUCTURE OF O-ACETYLSERINE SULFHYDRYLASE (OASS) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH THE REACTION INTERMEDIATE ALPHA-AMINOACRYLATE

Authors :   G. Schneider, R. Schnell

Date :   30 May 07 (Deposition) - 12 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Mycobacterium Tuberculosis, Pyridoxal-5'-Phosphate, Sulphur Metabolism, Cysteine Biosynthesis, Alpha-Aminoacrylate Intermediate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Schnell, W. Oehlmann, M. Singh, G. Schneider
Structural Insights Into Catalysis And Inhibition Of O-Acetylserine Sulfhydrylase From Mycobacterium Tuberculosis: Crystal Structures Of The Enzyme {Alpha}-Aminoacrylate Intermediate And An Enzyme-Inhibitor Complex.
J. Biol. Chem. V. 282 23473 2007
PubMed-ID: 17567578 | Reference-DOI: 10.1074/JBC.M703518200

Molecule 1 - CYSTEINE SYNTHASE A
	Chains	:	A
	EC Number	:	2.5.1.47
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CYSK
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	RV2334
	Synonym	:	O-ACETYLSERINE SULFHYDRYLASE A, O-ACETYLSERINE THIOL, LYASE A, CSASE A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	PDA	1	Ligand/Ion	2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	PDA	2	Ligand/Ion	2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:44 , THR A:71 , SER A:72 , GLY A:73 , ASN A:74 , THR A:75 , GLN A:144 , VAL A:177 , GLY A:178 , THR A:179 , GLY A:180 , GLY A:181 , THR A:182 , GLY A:222 , ILE A:223 , SER A:266 , PRO A:293 , ASP A:294 , TYR A:299 , HOH A:322 , HOH A:338 , HOH A:346 , HOH A:351	BINDING SITE FOR RESIDUE PDA A 311
2	AC2	SOFTWARE	GLN A:57 , ASP A:247 , GLN A:276 , ARG A:279	BINDING SITE FOR RESIDUE MPD A 312

(no "SS Bond" information available for 2Q3D)

(no "Cis Peptide Bond" information available for 2Q3D)

(no "SAP(SNP)/Variant" information available for 2Q3D)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYS_SYNTHASE	PS00901	Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.	CYSK_MYCTO	33-51	1	A:33-51
1	CYS_SYNTHASE	PS00901		CYSK_MYCTU	33-51	1	A:33-51

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYS_SYNTHASE	PS00901	Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.	CYSK_MYCTO	33-51	2	A:33-51
1	CYS_SYNTHASE	PS00901		CYSK_MYCTU	33-51	2	A:33-51

(no "Exon" information available for 2Q3D)

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:306
 aligned with CYSK_MYCTO | P9WP54 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      
           CYSK_MYCTO     1 MSIAEDITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGLIKPDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGADGMSGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTGGTITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEIITVGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYLSTPLFA 306
               SCOP domains d2q3da_ A: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2q3dA01 A:1-44,A:147-306                    2q3dA02 A:45-146  [code=3.40.50.1100, no name defined]                                                2q3dA01 A:1-44,A:147-306  [code=3.40.50.1100, no name defined]                                                                                                   CATH domains
               Pfam domains ------PALP-2q3dA01 A:7-294                                                                                                                                                                                                                                                                            ------------ Pfam domains
         Sec.struct. author .....hhhhhh....eee..........eeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee..................................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------CYS_SYNTHASE       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q3d A   1 MSIAEDITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGLIKPDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGADGMSGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTGGTITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEIITVGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYLSTPLFA 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Chain A from PDB  Type:PROTEIN  Length:306
 aligned with CYSK_MYCTU | P9WP55 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      
           CYSK_MYCTU     1 MSIAEDITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGLIKPDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGADGMSGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTGGTITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEIITVGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYLSTPLFA 306
               SCOP domains d2q3da_ A: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2q3dA01 A:1-44,A:147-306                    2q3dA02 A:45-146  [code=3.40.50.1100, no name defined]                                                2q3dA01 A:1-44,A:147-306  [code=3.40.50.1100, no name defined]                                                                                                   CATH domains
               Pfam domains ------PALP-2q3dA01 A:7-294                                                                                                                                                                                                                                                                            ------------ Pfam domains
         Sec.struct. author .....hhhhhh....eee..........eeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee..................................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------CYS_SYNTHASE       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q3d A   1 MSIAEDITQLIGRTPLVRLRRVTDGAVADIVAKLEFFNPANSVKDRIGVAMLQAAEQAGLIKPDTIILEPTSGNTGIALAMVCAARGYRCVLTMPETMSLERRMLLRAYGAELILTPGADGMSGAIAKAEELAKTDQRYFVPQQFENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTGGTITGVAQVIKERKPSARFVAVEPAASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEIITVGNEDALNVARRLAREEGLLVGISSGAATVAALQVARRPENAGKLIVVVLPDFGERYLSTPLFA 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1100, no name defined] (77)

Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: rv2334. (3)

1a	2q3dA01	A:1-44,A:147-306
1b	2q3dA02	A:45-146

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PALP] (67)

Family: PALP (67)

Mycobacterium tuberculosis (4)

PALP-2q3dA01

A:7-294

Asymmetric Unit(hide GO term definitions)

Chain A (CYSK_MYCTO | P9WP54)

molecular function
	GO:0004124	cysteine synthase activity	Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.
	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:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019344	cysteine biosynthetic process	The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
	GO:0006535	cysteine biosynthetic process from serine	The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.

Chain A (CYSK_MYCTU | P9WP55)

molecular function
	GO:0080146	L-cysteine desulfhydrase activity	Catalysis of the reaction: L-cysteine + H2O = ammonia + pyruvate + hydrogen sulfide + H+.
	GO:0004124	cysteine synthase activity	Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.
	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: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:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019344	cysteine biosynthetic process	The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
	GO:0006535	cysteine biosynthetic process from serine	The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.
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.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	CYSK_MYCTO \| P9WP54	:	2q3b 2q3c 3zei
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Ligands, Modified Residues, Ions (2, 2)

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