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(-) Description

Title :  CRYSTAL STRUCTURE OF O-PHOSPHOSERINE SULFHYDRYLASE
 
Authors :  Y. Oda, K. Mino, K. Ishikawa, M. Ataka
Date :  09 Jun 04  (Deposition) - 28 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homodimer, Open Alpha/Beta Folding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Oda, K. Mino, K. Ishikawa, M. Ataka
Three-Dimensional Structure Of A New Enzyme, O-Phosphoserin Sulfhydrylase, Involved In L-Cysteine Biosynthesis By A Hyperthermophilic Archaeon, Aeropyrum Pernix K1, At 2. 0A Resolution
J. Mol. Biol. V. 351 334 2005
PubMed-ID: 16005886  |  Reference-DOI: 10.1016/J.JMB.2005.05.064

(-) Compounds

Molecule 1 - CYSTEINE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAPE1586
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APE1586
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: K1
    Synonym: O-PHOSPHOSERINE SULFHYDRYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:152 , SER A:153 , THR A:203 , GLN A:224 , PHE A:225 , HOH A:1417 , HOH A:1470BINDING SITE FOR RESIDUE ACT A 1401
2AC2SOFTWARELYS B:127 , THR B:152 , SER B:153 , GLN B:224 , HOH B:2413 , HOH B:2519BINDING SITE FOR RESIDUE ACT B 2401
3AC3SOFTWARELYS A:127 , ASN A:155 , SER A:259 , 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 , HOH A:1402 , HOH A:1412 , HOH A:1415BINDING SITE FOR RESIDUE PLP A 400
4AC4SOFTWARELYS B:127 , ASN B:155 , SER B:259 , LEU B:260 , GLY B:261 , THR B:262 , SER B:263 , GLY B:264 , HIS B:265 , ILE B:296 , SER B:341 , PRO B:368 , ASP B:369 , HOH B:2402 , HOH B:2407 , HOH B:2409BINDING SITE FOR RESIDUE PLP B 400

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:36 -A:64
2B:36 -B:64

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:95 -Pro A:96
2Lys B:95 -Pro B:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYS_SYNTHASEPS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.CYSO_AERPE115-134
 		  2A:115-134
B:115-134

(-) Exons   (0, 0)

(no "Exon" information available for 1WKV)

(-) Sequences/Alignments

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: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 d1wkva1 A:2-383 O-acetylserine sulfhydrylase (Cysteine synthase)                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhh....hhhhhhhhhhhheee...hhhhhhhhhhhhhhhh..eee.....eee...............ee.hhhhhhhhh....eee........eeeeeee.hhh......hhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh...eeeeeee..........hhhhh.hhhhhh....eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------CYS_SYNTHASE        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wkv A   2 ALADISGYLDVLDSVRGFSYLENAREVLRSGEARCLGNPRSEPEYVKALYVIGASRIPVGDGCSHTLEELGVFDISVPGEMVFPSPLDFFERGKPTPLVRSRLQLPNGVRVWLKLEWYNPFSLSVKDRPAVEIISRLSRRVEKGSLVADATSSNFGVALSAVARLYGYRARVYLPGAAEEFGKLLPRLLGAQVIVDPEAPSTVHLLPRVMKDSKNEGFVHVNQFYNDANFEAHMRGTAREIFVQSRRGGLALRGVAGSLGTSGHMSAAAFYLQSVDPSIRAVLVQPAQGDSIPGIRRVETGMLWINMLDISYTLAEVTLEEAMEAVVEVARSDGLVIGPSGGAAVKALAKKAAEGDLEPGDYVVVVPDTGFKYLSLVQNALE 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 d1wkvb_ B: O-acetylserine sulfhydrylase (Cysteine synthase)                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------PALP-1wkvB01 B:91-371                                                                                                                                                                                                                                                                    ------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------PALP-1wkvB02 B:91-371                                                                                                                                                                                                                                                                    ------------- Pfam domains (2)
         Sec.struct. author .eee.hhhhhhhhhh....hhhhhhhhhhhheee...hhhhhhhhhhhhhhhh..eee.....eee...............ee.hhhhhhhhh....eee........eeeeeee.hhh......hhhhhhhhhhh.........eeeee.hhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh...eeeeeee..........hhhhh.hhhhhh....eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------CYS_SYNTHASE        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wkv B   2 ALADISGYLDVLDSVRGFSYLENAREVLRSGEARCLGNPRSEPEYVKALYVIGASRIPVGDGCSHTLEELGVFDISVPGEMVFPSPLDFFERGKPTPLVRSRLQLPNGVRVWLKLEWYNPFSLSVKDRPAVEIISRLSRRVEKGSLVADATSSNFGVALSAVARLYGYRARVYLPGAAEEFGKLLPRLLGAQVIVDPEAPSTVHLLPRVMKDSKNEGFVHVNQFYNDANFEAHMRGTAREIFVQSRRGGLALRGVAGSLGTSGHMSAAAFYLQSVDPSIRAVLVQPAQGDSIPGIRRVETGMLWINMLDISYTLAEVTLEEAMEAVVEVARSDGLVIGPSGGAAVKALAKKAAEGDLEPGDYVVVVPDTGFKYLSLVQNALEG 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WKV)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PALP] (67)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological 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.

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 Related Entries

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UniProtKB/Swiss-Prot
        CYSO_AERPE | Q9YBL2: 3vsa 3vsc 3vsd 5b36 5b3a

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