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(-) Description

Title :  CYSTATHIONINE GAMMA-SYNTHASE (CGS) FROM ESCHERICHIA COLI
 
Authors :  T. Clausen, A. Messerschmidt
Date :  23 Sep 98  (Deposition) - 27 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lyase, Llp-Dependent Enzymes, Methionine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Clausen, R. Huber, L. Prade, M. C. Wahl, A. Messerschmidt
Crystal Structure Of Escherichia Coli Cystathionine Gamma-Synthase At 1. 5 A Resolution.
Embo J. V. 17 6827 1998
PubMed-ID: 9843488  |  Reference-DOI: 10.1093/EMBOJ/17.23.6827
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CYSTATHIONINE GAMMA-SYNTHASE)
    Chains: A, B, C, D
    EC Number: 4.2.99.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21/DE3
    Expression System Taxid: 469008
    Expression System Vector: PET22B
    Gene: METB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: PLP BOUND AS COFACTOR TO LYS 198
    Strain: DH5
    Synonym: CGS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1DHD1Ligand/Ion2,4-DIOXO-PENTANEDIOIC ACID
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA D:157 , LYS D:158 , HIS D:161 , HOH D:1654 , HOH D:1664BINDING SITE FOR RESIDUE DHD D 1501
2PLAAUTHORLLP A:198COFACTOR SITE CHAIN A
3PLBAUTHORLLP B:198COFACTOR SITE CHAIN B
4PLCAUTHORLLP C:198COFACTOR SITE CHAIN C
5PLDAUTHORLLP D:198COFACTOR SITE CHAIN D

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CS1)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:145 -Pro A:146
2Asn A:148 -Pro A:149
3Ser B:145 -Pro B:146
4Asn B:148 -Pro B:149
5Ser C:145 -Pro C:146
6Asn C:148 -Pro C:149
7Ser D:145 -Pro D:146
8Asn D:148 -Pro D:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CS1)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYS_MET_METAB_PPPS00868 Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.METB_ECOLI190-204
 
 
 		  4A:190-204
B:190-204
C:190-204
D:190-204

(-) Exons   (0, 0)

(no "Exon" information available for 1CS1)

(-) 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:384
 aligned with METB_ECOLI | P00935 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:384
                                    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       322       332       342       352       362       372       382    
           METB_ECOLI     3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRAANKG 386
               SCOP domains d1cs1a_ A: Cystathionine gamma-synthase, CGS                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1cs1A01 A:3-247 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                  1cs1A02 A:248-386 Aspartate Aminotransferase, domain 1                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhh........................................hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeee...........hhhhhhhhhhh..eeeee..........hhhh...eeeee.............eeeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhh......eeeeee...hhhhhhhhhh...............eeeehhh.......hhhhhhh.....eeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cs1 A   3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLALGADLVLHSCTkYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRAANKG 386
                                    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       322       332       342       352       362       372       382    
                                                                                                                                                                                                                             198-LLP                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:384
 aligned with METB_ECOLI | P00935 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:384
                                    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       322       332       342       352       362       372       382    
           METB_ECOLI     3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRAANKG 386
               SCOP domains d1cs1b_ B: Cystathionine gamma-synthase, CGS                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1cs1B01 B:3-247 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                  1cs1B02 B:248-386 Aspartate Aminotransferase, domain 1                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhh........................................hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeee............hhhhhhhhhhh..eeeee.................eeeee.............eeeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhh......eeeeee...hhhhhhhhhh...............eeee..........hhhhhh......eeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cs1 B   3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLALGADLVLHSCTkYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRAANKG 386
                                    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       322       332       342       352       362       372       382    
                                                                                                                                                                                                                             198-LLP                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:384
 aligned with METB_ECOLI | P00935 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:384
                                    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       322       332       342       352       362       372       382    
           METB_ECOLI     3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRAANKG 386
               SCOP domains d1cs1c_ C: Cystathionine gamma-synthase, CGS                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1cs1C01 C:3-247 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                  1cs1C02 C:248-386 Aspartate Aminotransferase, domain 1                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhh........................................hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.....eeeee....hhhhhhhhhh...eeee............hhhhhhhhhhh..eeeee....hhhh.........eeeee.............eeeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhh......eeeeee...hhhhhhhhhh...............eeee..........hhhhhh......eeeee.....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cs1 C   3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLALGADLVLHSCTkYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRAANKG 386
                                    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       322       332       342       352       362       372       382    
                                                                                                                                                                                                                             198-LLP                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:384
 aligned with METB_ECOLI | P00935 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:384
                                    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       322       332       342       352       362       372       382    
           METB_ECOLI     3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRAANKG 386
               SCOP domains d1cs1d_ D: Cystathionine gamma-synthase, CGS                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1cs1D01 D:3-247 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                  1cs1D02 D:248-386 Aspartate Aminotransferase, domain 1                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhh........................................hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.....eeeee....hhhhhhhhhh...eeeee...........hhhhhhhhhhh..eeeee..........hhhh...eeeee.............eeeee..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhh......eeeeee...hhhhhhhhhh...............eeee..........hhhhhh......eeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cs1 D   3 RKQATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPLALGADLVLHSCTkYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELDGDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLENGFRAANKG 386
                                    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       322       332       342       352       362       372       382    
                                                                                                                                                                                                                             198-LLP
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 4)

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

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CS1)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (METB_ECOLI | P00935)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0003962    cystathionine gamma-synthase activity    Catalysis of the reaction: O-succinyl-L-homoserine + L-cysteine = cystathionine + succinate.
    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:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
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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