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(-) Description

Title :  CRYSTAL STRUCTURE OF O-PHOSHOSERINE SULFHYDRYLASE FROM AEROPYRUM PERNIX IN COMPLEXED WITH THE ALPHA-AMINOACRYLATE INTERMEDIATE
 
Authors :  T. Nakamura, E. Takeda, Y. Kawai, M. Kataoka, K. Ishikawa
Date :  12 Feb 16  (Deposition) - 16 Mar 16  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cysteine Biosynthesis, Sulfhydrylase, Intermediate, External Schiff Base Of Plp With Alpha-Amino Acrylate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Takeda, K. Kunimoto, Y. Kawai, M. Kataoka, K. Ishikawa, T. Nakamura
Role Of F225 In O-Phosphoserine Sulfhydrylase From Aeropyru Pernix K1
Extremophiles V. 20 733 2016
PubMed-ID: 27377295  |  Reference-DOI: 10.1007/S00792-016-0862-6
(for further references see the PDB file header)

(-) Compounds

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: CYSO, APE_1586
    Organism Scientific: AEROPYRUM PERNIX K1
    Organism Taxid: 272557
    Strain: K1
    Synonym: CYSTATHIONINE BETA-SYNTHASE,CYSTEINE SYNTHASE,O-ACETYLSERINE SULFHYDRYLASE,O-PHOSPHOSERINE SULFHYDRYLASE,SERINE SULFHYDRASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
10JO2Ligand/Ion2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOICACID
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
10JO1Ligand/Ion2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOICACID
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
10JO1Ligand/Ion2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOICACID
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:82 , GLY A:94 , PRO A:96 , THR A:97 , HOH A:535 , HOH A:568 , TYR B:119binding site for residue MPD A 401
2AC2SOFTWARELYS A:127 , THR A:152 , SER A:153 , ASN A:155 , PHE A:156 , GLN A:224 , 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 , TYR A:374 , HOH A:541 , HOH A:546 , HOH A:591binding site for residue 0JO A 402
3AC3SOFTWAREARG A:332 , SER B:65 , ARG B:165 , HOH B:515 , HOH B:592binding site for residue MPD B 401
4AC4SOFTWARELYS B:127 , THR B:152 , SER B:153 , ASN B:155 , PHE B:156 , GLN B:224 , 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 , ASP B:369 , TYR B:374 , HOH B:556 , HOH B:563 , HOH B:569binding site for residue 0JO B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B3A)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:95 -Pro A:96
2Lys B:95 -Pro B:96
3Ser B:139 -Arg B:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B3A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B3A)

(-) Exons   (0, 0)

(no "Exon" information available for 5B3A)

(-) Sequences/Alignments

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
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhh....hhhhhhhhhhhhee....hhhhhhhhhhhhhhh...eee......ee...............ee.hhhhhhhhh....eee....hhh.eeeeeee..........hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh...eeeeeee...............hhhhhhh....eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b3a 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
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhh...hhhhhhhhhhhhhee....hhhhhhhhhhhhhhhh..eee......ee...............ee.hhhhhhhhh....eee........eeeeeee.hhh......hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh...eeeeeee...............hhhhhhh....eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b3a 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  (0, 0)

(no "SCOP Domain" information available for 5B3A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B3A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B3A)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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        CYSO_AERPE | Q9YBL2: 1wkv 3vsa 3vsc 3vsd 5b36

(-) Related Entries Specified in the PDB File

5b36