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(-) Description

Title :  2.05 A CRYSTAL STRUCTURE OF CYSM FROM MYCOBACTERIUM TUBERCULOSIS - OPEN AND CLOSED CONFORMATIONS
 
Authors :  D. Agren, R. Schnell, G. Schneider
Date :  08 Dec 08  (Deposition) - 23 Dec 08  (Release) - 10 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cysteine Synthase, Cysm, Tuberculosis, Cyso, O- Phosphoserine, Amino-Acid Biosynthesis, Cysteine Biosynthesis, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Agren, R. Schnell, G. Schneider
The C-Terminal Of Cysm From Mycobacterium Tuberculosis Protects The Aminoacrylate Intermediate And Is Involved In Sulfur Donor Selectivity
Febs Lett. V. 583 330 2009
PubMed-ID: 19101553  |  Reference-DOI: 10.1016/J.FEBSLET.2008.12.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYSTEINE SYNTHASE B
    Chains: A, B
    EC Number: 2.5.1.65
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CYSM (RV1336)
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: CYSM, O-ACETYLSERINE SULFHYDRYLASE B, CSASE B, O- ACETYLSERINE (THIOL)-LYASE B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (0, 0)

(no "Site" information available for 3FGP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FGP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FGP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYS_SYNTHASEPS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site.CYSM_MYCTO40-58
 		  2A:40-58
B:40-58
CYSM_MYCTU40-58
 		  2A:40-58
B:40-58

(-) Exons   (0, 0)

(no "Exon" information available for 3FGP)

(-) 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:312
 aligned with CYSM_MYCTO | P9WP52 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  
           CYSM_MYCTO     3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAE 314
               SCOP domains d3fgpa_ A: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.....eee................eeeeeee.hhh.....hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------CYS_SYNTHASE       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fgp A   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIkDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAE 314
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  
                                                                           51-LLP                                                                                                                                                                                                                                                                   


Chain A from PDB  Type:PROTEIN  Length:312
 aligned with CYSM_MYCTU | P9WP53 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:312
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  
           CYSM_MYCTU     3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAE 314
               SCOP domains d3fgpa_ A: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.....eee................eeeeeee.hhh.....hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------CYS_SYNTHASE       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fgp A   3 RYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIkDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAE 314
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  
                                                                           51-LLP                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with CYSM_MYCTO | P9WP52 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:324
                             1                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319    
           CYSM_MYCTO     - -MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAETALEGQLWA 323
               SCOP domains d3fgpb_ B: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.hhhhh.....eeee...............eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh..eeee........hhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhh.................eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhh....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ----------------------------------------CYS_SYNTHASE       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fgp B   0 HMARYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIkDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAETALEGQLWA 323
                                     9        19        29        39        49 |      59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319    
                                                                              51-LLP                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with CYSM_MYCTU | P9WP53 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:324
                             1                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319    
           CYSM_MYCTU     - -MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAETALEGQLWA 323
               SCOP domains d3fgpb_ B: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.hhhhh.....eeee...............eeeeeee.........hhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh..eeee........hhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.....eeeeeee....hhhhhh.................eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhh....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------CYS_SYNTHASE       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fgp B   0 HMARYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIkDRPAVRMIEQAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPEITHFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPRYGEGVYALRNMDEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKYLSTGAYAGSLDDAETALEGQLWA 323
                                     9        19        29        39        49 |      59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319    
                                                                              51-LLP
   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 3FGP)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CYSM_MYCTO | P9WP52)
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,B   (CYSM_MYCTU | P9WP53)
molecular function
    GO:0033847    O-phosphoserine sulfhydrylase activity    Catalysis of the reaction: O-phospho-L-serine + hydrogen sulfide = L-cysteine + phosphate.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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  2.5.1.65
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYSM_MYCTO | P9WP52: 3dki 3dwg 3dwi 5i7a
        CYSM_MYCTU | P9WP53: 3dki 3dwg 3dwi 5i6d 5i7a 5i7h 5i7o 5i7r 5iw8 5iwc

(-) Related Entries Specified in the PDB File

3dki 2.1 A X-RAY STRUCTURE OF CYSM (RV1336) FROM MYCOBACTERIUM TUBERCULOSIS AN O-PHOSPHOSERINE DEPENDENT CYSTEINE SYNTHASE