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(-) Description

Title :  CRYSTAL STRUCTURE OF O-ACETYLSERINE SULFHYDRYLASE B
 
Authors :  M. T. Claus, G. E. Zocher, T. H. P. Maier, G. E. Schulz
Date :  18 Jan 05  (Deposition) - 22 Jun 05  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cysteine Biosynthesis, Plp-Dependent Enzyme, Pyridoxal-5'- Phosphate, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. T. Claus, G. E. Zocher, T. H. P. Maier, G. E. Schulz
Structure Of The O-Acetylserine Sulfhydrylase Isoenzyme Cysm From Escherichia Coli
Biochemistry V. 44 8620 2005
PubMed-ID: 15952768  |  Reference-DOI: 10.1021/BI050485+

(-) Compounds

Molecule 1 - CYSTEINE SYNTHASE B
    Chains: A, B, C, D
    EC Number: 2.5.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-IBA3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: SCHIFF BASE LINK BETWEEN A41 AND PLP320
    Synonym: O-ACETYLSERINE SULFHYDRYLASE B, O-ACETYLSERINE (THIOL)-LYASE B, CSASE B, O-ACETYLSERINE SULFHYDRYLASE B

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:41 , ASN A:71 , SER A:172 , MET A:173 , GLY A:174 , THR A:175 , THR A:176 , GLY A:177 , THR A:178 , GLY A:208 , SER A:255 , CYS A:280 , TYR A:286 , HOH A:2015BINDING SITE FOR RESIDUE PLP A 320
2AC2SOFTWARELYS B:41 , ASN B:71 , SER B:172 , MET B:173 , GLY B:174 , THR B:175 , THR B:176 , GLY B:177 , THR B:178 , GLY B:208 , ILE B:209 , SER B:255 , TYR B:286 , HOH B:2010BINDING SITE FOR RESIDUE PLP B 320
3AC3SOFTWARELYS C:41 , ASN C:71 , SER C:172 , MET C:173 , GLY C:174 , THR C:175 , THR C:176 , GLY C:177 , THR C:178 , PRO C:207 , GLY C:208 , ILE C:209 , SER C:255 , ASP C:281 , HOH C:2009 , HOH C:2010 , HOH C:2036BINDING SITE FOR RESIDUE PLP C 320
4AC4SOFTWAREVAL D:40 , LYS D:41 , GLY D:174 , THR D:175 , THR D:176 , GLY D:177 , THR D:178 , SER D:255 , CYS D:280 , TYR D:286 , HOH D:2014 , HOH D:2015BINDING SITE FOR RESIDUE PLP D 320

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg B:123 -Asp B:124
2Glu B:128 -Met B:129
3Trp B:212 -Pro B:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYS_SYNTHASEPS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.CYSM_ECOLI30-48
 
 
 		  4A:30-48
B:30-48
C:30-48
D:30-48
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYS_SYNTHASEPS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.CYSM_ECOLI30-48
 
 
 		  2A:30-48
B:30-48
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYS_SYNTHASEPS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.CYSM_ECOLI30-48
 
 
 		  2-
-
C:30-48
D:30-48

(-) Exons   (0, 0)

(no "Exon" information available for 2BHT)

(-) 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:294
 aligned with CYSM_ECOLI | P16703 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:294
                                    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    
           CYSM_ECOLI     1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGVSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGE 294
               SCOP domains -d2bhta1 A:2-293 O-acetylserine sulfhydrylase (Cysteine synthase)                                                                                                                                                                                                                                    - SCOP domains
               CATH domains 2bhtA01 A:1-34,A:154-294          2bhtA02 A:35-140  [code=3.40.50.1100, no name defined]                                                    -------------2bhtA01 A:1-34,A:154-294  [code=3.40.50.1100, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh....eee...........eeeee.hhh....hhhhhhhhhhhhhh.........eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh....ee......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh....eeeeeee............hhhhh....hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------CYS_SYNTHASE       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bht A   1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGRIKPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDLALEMANRGEGKLLDQFNNPDNPKAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGVSEFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGE 294
                                    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    


Chain B from PDB  Type:PROTEIN  Length:281
 aligned with CYSM_ECOLI | P16703 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:296
                                    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      
           CYSM_ECOLI     1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGVSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGEEH 296
               SCOP domains d2bhtb_ B: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2bhtB01 B:1-34,B:154-296          2bhtB02 B:35-140  [code=3.40.50.1100, no name defined]                                                    -------------2bhtB01 B:1-34,B:154-296  [code=3.40.50.1100, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh....eee..........eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhhh.eeee.....----....hhhhh....--------.....---........ee......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhh.....eeeeeee...........................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------CYS_SYNTHASE       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bht B   1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGRIKPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDN----RRAAMRAYGAELI--------EGARD---EMANRGEGKLLDQFNNPDNPKAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGVSEFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGEEH 296
                                    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      
                                                                                                                        94   99         111      120 124 128                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:292
 aligned with CYSM_ECOLI | P16703 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:292
                                    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  
           CYSM_ECOLI     1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGVSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVF 292
               SCOP domains d2bhtc_ C: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2bhtC01 C:1-34,C:154-292          2bhtC02 C:35-140  [code=3.40.50.1100, no name defined]                                                    -------------2bhtC01 C:1-34,C:154-292  [code=3.40.50.1100, no name defined]                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh....eee..........eeeeee........hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh...ee........hhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhh......eeeeeee............hhhhh....hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh........eeeeee...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------CYS_SYNTHASE       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bht C   1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGRIKPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDLALEMANRGEGKLLDQFNNPDNPKAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGVSEFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVF 292
                                    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  


Chain D from PDB  Type:PROTEIN  Length:285
 aligned with CYSM_ECOLI | P16703 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:296
                                    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      
           CYSM_ECOLI     1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDLALEMANRGEGKLLDQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGVSRFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGEEH 296
               SCOP domains d2bhtd_ D: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2bhtD01 D:1-34,D:154-296          2bhtD02 D:35-140  [code=3.40.50.1100, no name defined]                                                    -------------2bhtD01 D:1-34,D:154-296  [code=3.40.50.1100, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eee..........eeeeee........hhhhhhhhhhhhhhhh.......eee....hhhhhhhhhhhhhhh.eee.....----hhhhhhhh......-------.....hhhhhhhh............hhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh.....eeeeeee...........................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------CYS_SYNTHASE       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bht D   1 MSTLEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGRIKPGDVLIEATSGNTGIALAMIAALKGYRMKLLMPD----ERRAAMRAYGAELI-------MEGARDLALEMANRGEGKLLDQFNNPDNPKAHYTTTGPEIWQQTGGRITHFVSSMGTTGTITGVSEFMREQSKPVTIVGLQPEEGSSIPGIRRWPTEYLPGIFNASLVDEVLDIHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVAKANPDAVVVAIICDRGDRYLSTGVFGEEH 296
                                    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      
                                                                                                                       93   98          111     119
   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  (2, 4)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
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)
(-)
Escherichia coli. Organism_taxid: 562. (4)
1a2bhtC01C:1-34,C:154-292
1b2bhtA02A:35-140
1c2bhtC02C:35-140
1d2bhtD02D:35-140
1e2bhtB02B:35-140
1f2bhtA01A:1-34,A:154-294
1g2bhtB01B:1-34,B:154-296
1h2bhtD01D:1-34,D:154-296

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BHT)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CYSM_ECOLI | P16703)
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: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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CYSM_ECOLI | P16703: 2bhs 2v03

(-) Related Entries Specified in the PDB File

2bhs CRYSTAL STRUCTURE OF CYSTEINE SYNTHASE B