3VSC - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE K127A MUTANT OF O-PHOSPHOSERINE SULFHYDRYLASE COMPLEXED WITH EXTERNAL SCHIFF BASE OF PYRIDOXAL 5'-PHOSPHATE WITH O-PHOSPHO-L-SERINE

Authors :   T. Nakamura, Y. Kawai, M. Kataoka, K. Ishikawa

Date :   24 Apr 12 (Deposition) - 16 May 12 (Release) - 16 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.07

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Cysteine Biosynthesis, External Schiff Base Of Plp With O- Phosphoserine, K127A Mutant, Sulfhydrylase (Inactivated), Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nakamura, Y. Kawai, K. Kunimoto, Y. Iwasaki, K. Nishii, M. Kataoka, K. Ishikawa
Structural Analysis Of The Substrate Recognition Mechanism In O-Phosphoserine Sulfhydrylase From The Hyperthermophilic Archaeon Aeropyrum Pernix K1
J. Mol. Biol. V. 422 33 2012
PubMed-ID: 22580223 | Reference-DOI: 10.1016/J.JMB.2012.05.009
(for further references see the PDB file header)

Molecule 1 - PROTEIN CYSO
	Chains	:	A, B
	EC Number	:	4.2.1.22, 2.5.1.47, 2.5.1.65
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3D
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	APE1586, APE_1586, CYSO
	Mutation	:	YES
	Organism Scientific	:	AEROPYRUM PERNIX
	Organism Taxid	:	272557
	Strain	:	K1
	Synonym	:	CYSTATHIONINE BETA-SYNTHASE, CYSTEINE SYNTHASE, O- ACETYLSERINE SULFHYDRYLASE, O-PHOSPHOSERINE SULFHYDRYLASE, SERINE SULFHYDRASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SEP	2	Mod. Residue	PHOSPHOSERINE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SEP	1	Mod. Residue	PHOSPHOSERINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SEP	1	Mod. Residue	PHOSPHOSERINE

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SEP	2	Mod. Residue	PHOSPHOSERINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:155 , SER A:259 , LEU A:260 , GLY A:261 , THR A:262 , SER A:263 , GLY A:264 , HIS A:265 , GLY A:295 , ILE A:296 , SER A:341 , PRO A:368 , ASP A:369 , TYR A:374 , SEP A:402 , HOH A:502 , HOH A:516 , HOH A:532 , HOH A:569	BINDING SITE FOR RESIDUE PLP A 401
2	AC2	SOFTWARE	THR A:152 , SER A:153 , ASN A:155 , PHE A:156 , THR A:203 , GLN A:224 , PHE A:225 , GLY A:261 , THR A:262 , GLY A:295 , PLP A:401	BINDING SITE FOR RESIDUE SEP A 402
3	AC3	SOFTWARE	MET A:82 , GLY A:94 , PRO A:96 , THR A:97 , MET B:82 , TYR B:119 , HOH B:524	BINDING SITE FOR RESIDUE MPD A 403
4	AC4	SOFTWARE	ASN B:155 , SER B:259 , GLY B:261 , THR B:262 , SER B:263 , GLY B:264 , HIS B:265 , GLY B:295 , ILE B:296 , SER B:341 , PRO B:368 , TYR B:374 , SEP B:402 , HOH B:501 , HOH B:541 , HOH B:567	BINDING SITE FOR RESIDUE PLP B 401
5	AC5	SOFTWARE	THR B:152 , SER B:153 , ASN B:155 , PHE B:156 , THR B:203 , GLN B:224 , PHE B:225 , GLY B:261 , THR B:262 , GLY B:295 , ARG B:297 , PLP B:401	BINDING SITE FOR RESIDUE SEP B 402

Asymmetric Unit

No.	Residues
1	A:36	-	A:64
2	B:36	-	B:64

Asymmetric Unit

No.	Residues
1	Lys A:95	-	Pro A:96
2	Lys B:95	-	Pro B:96

(no "SAP(SNP)/Variant" information available for 3VSC)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYS_SYNTHASE	PS00901	Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.	CYSO_AERPE	115-134	2	A:115-134 B:115-134

Biological Unit 1 (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.	CYSO_AERPE	115-134	1	A:115-134 -

Biological Unit 2 (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.	CYSO_AERPE	115-134	1	- B:115-134

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYS_SYNTHASE	PS00901	Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.	CYSO_AERPE	115-134	2	A:115-134 B:115-134

(no "Exon" information available for 3VSC)

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:382
 aligned with CYSO_AERPE | Q9YBL2 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:382
                                    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  
           CYSO_AERPE     2 ALADISGYLDVLDSVRGFSYLENAREVLRSGEARCLGNPRSEPEYVKALYVIGASRIPVGDGCSHTLEELGVFDISVPGEMVFPSPLDFFERGKPTPLVRSRLQLPNGVRVWLKLEWYNPFSLSVKDRPAVEIISRLSRRVEKGSLVADATSSNFGVALSAVARLYGYRARVYLPGAAEEFGKLLPRLLGAQVIVDPEAPSTVHLLPRVMKDSKNEGFVHVNQFYNDANFEAHMRGTAREIFVQSRRGGLALRGVAGSLGTSGHMSAAAFYLQSVDPSIRAVLVQPAQGDSIPGIRRVETGMLWINMLDISYTLAEVTLEEAMEAVVEVARSDGLVIGPSGGAAVKALAKKAAEGDLEPGDYVVVVPDTGFKYLSLVQNALE 383
               SCOP domains d3vsca_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhh....hhhhhhhhhhhheee...hhhhhhhhhhhhhhhh..eee.....eee...............ee.hhhhhhhhh....eee....hhh.eeeeeee.hhh......hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------CYS_SYNTHASE        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vsc A   2 ALADISGYLDVLDSVRGFSYLENAREVLRSGEARCLGNPRSEPEYVKALYVIGASRIPVGDGCSHTLEELGVFDISVPGEMVFPSPLDFFERGKPTPLVRSRLQLPNGVRVWLKLEWYNPFSLSVADRPAVEIISRLSRRVEKGSLVADATSSNFGVALSAVARLYGYRARVYLPGAAEEFGKLLPRLLGAQVIVDPEAPSTVHLLPRVMKDSKNEGFVHVNQFYNDANFEAHMRGTAREIFVQSRRGGLALRGVAGSLGTSGHMSAAAFYLQSVDPSIRAVLVQPAQGDSIPGIRRVETGMLWINMLDISYTLAEVTLEEAMEAVVEVARSDGLVIGPSGGAAVKALAKKAAEGDLEPGDYVVVVPDTGFKYLSLVQNALE 383
                                    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

Chain B from PDB  Type:PROTEIN  Length:383
 aligned with CYSO_AERPE | Q9YBL2 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:383
                                    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   
           CYSO_AERPE     2 ALADISGYLDVLDSVRGFSYLENAREVLRSGEARCLGNPRSEPEYVKALYVIGASRIPVGDGCSHTLEELGVFDISVPGEMVFPSPLDFFERGKPTPLVRSRLQLPNGVRVWLKLEWYNPFSLSVKDRPAVEIISRLSRRVEKGSLVADATSSNFGVALSAVARLYGYRARVYLPGAAEEFGKLLPRLLGAQVIVDPEAPSTVHLLPRVMKDSKNEGFVHVNQFYNDANFEAHMRGTAREIFVQSRRGGLALRGVAGSLGTSGHMSAAAFYLQSVDPSIRAVLVQPAQGDSIPGIRRVETGMLWINMLDISYTLAEVTLEEAMEAVVEVARSDGLVIGPSGGAAVKALAKKAAEGDLEPGDYVVVVPDTGFKYLSLVQNALEG 384
               SCOP domains d3vscb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhh....hhhhhhhhhhhheee...hhhhhhhhhhhhhhh...eee.....eee...............ee.hhhhhhhhh....eee....hhh.eeeeeee.hhh......hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------CYS_SYNTHASE        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vsc B   2 ALADISGYLDVLDSVRGFSYLENAREVLRSGEARCLGNPRSEPEYVKALYVIGASRIPVGDGCSHTLEELGVFDISVPGEMVFPSPLDFFERGKPTPLVRSRLQLPNGVRVWLKLEWYNPFSLSVADRPAVEIISRLSRRVEKGSLVADATSSNFGVALSAVARLYGYRARVYLPGAAEEFGKLLPRLLGAQVIVDPEAPSTVHLLPRVMKDSKNEGFVHVNQFYNDANFEAHMRGTAREIFVQSRRGGLALRGVAGSLGTSGHMSAAAFYLQSVDPSIRAVLVQPAQGDSIPGIRRVETGMLWINMLDISYTLAEVTLEEAMEAVVEVARSDGLVIGPSGGAAVKALAKKAAEGDLEPGDYVVVVPDTGFKYLSLVQNALEG 384
                                    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

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 3VSC)

(no "Pfam Domain" information available for 3VSC)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYSO_AERPE | Q9YBL2)

molecular function
	GO:0033847	O-phosphoserine sulfhydrylase activity	Catalysis of the reaction: O-phospho-L-serine + hydrogen sulfide = L-cysteine + phosphate.
	GO:0004122	cystathionine beta-synthase activity	Catalysis of the reaction: L-serine + L-homocysteine = cystathionine + H2O.
	GO:0004124	cysteine synthase activity	Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
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	3vsc
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	2.5.1.47
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	2.5.1.65
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	4.2.1.22
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UniProtKB/Swiss-Prot
	CYSO_AERPE \| Q9YBL2	:	1wkv 3vsa 3vsd 5b36 5b3a

1wkv	CRYSTAL STRUCTURE OF O-PHOSPHOSERINE SULFHYDRYLASE
3vsa	CRYSTAL STRUCTURE OF O-PHOSPHOSERINE SULFHYDRYLASE WITHOUT ACETATE
3vsd

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Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

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