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(-) Description

Title :  CRYSTAL STRUCTURE OF CYSTATHIONINE BETA-SYNTHASE FROM LACTOBACILLUS PLANTARUM
 
Authors :  Y. Matoba, M. Sugiyama
Date :  04 Dec 15  (Deposition) - 07 Dec 16  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Biol. Unit 3:  D  (2x)
Keywords :  Enzyme, Plp, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Matoba, T. Yoshida, H. Izuhara-Kihara, M. Noda, M. Sugiyama
Crystallographic And Mutational Analyses Of Cystathionine Beta-Synthase In The H2 S-Synthetic Gene Cluster In Lactobacillus Plantarum
Protein Sci. V. 26 763 2017
PubMed-ID: 28127810  |  Reference-DOI: 10.1002/PRO.3123

(-) Compounds

Molecule 1 - CYSTATHIONINE BETA-SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-21A(+)
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CBS, LP_0256
    Organism Scientific: LACTOBACILLUS PLANTARUM WCFS1
    Organism Taxid: 220668
    Strain: WCFS1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (2x):  B  
Biological Unit 3 (2x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 30)

Asymmetric Unit (3, 30)
No.NameCountTypeFull Name
1GOL14Ligand/IonGLYCEROL
2LLP4Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3SO412Ligand/IonSULFATE ION
Biological Unit 1 (3, 17)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3SO48Ligand/IonSULFATE ION
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3SO44Ligand/IonSULFATE ION
Biological Unit 3 (3, 12)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3SO44Ligand/IonSULFATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:250 , HIS A:251 , ARG A:254binding site for residue SO4 A 401
02AC2SOFTWARESER A:135 , ASN A:136 , SO4 A:403 , HOH A:529 , LYS D:62 , ASN D:136binding site for residue SO4 A 402
03AC3SOFTWARELYS A:62 , ASN A:136 , SO4 A:402 , HOH A:525 , HOH A:530 , SER D:135 , ASN D:136binding site for residue SO4 A 403
04AC4SOFTWARETHR A:69 , ALA A:70 , GLY A:71 , ASN A:72 , THR A:73 , GLN A:142 , HOH A:544 , HOH A:548binding site for residue SO4 A 404
05AC5SOFTWAREMET A:1 , MET C:1binding site for residue GOL A 405
06AC6SOFTWAREHIS A:5 , GLN A:7 , GLN A:82 , ALA A:83 , HIS B:25 , ASN B:281 , PRO C:19 , ASP C:255 , HIS C:256 , HOH C:505binding site for residue GOL A 406
07AC7SOFTWARELEU A:54 , HIS A:84 , HOH A:531 , ASN B:24 , THR B:276binding site for residue GOL A 407
08AC8SOFTWARETHR A:169 , ALA A:280 , ASN A:281 , SER A:282binding site for residue GOL A 408
09AC9SOFTWAREARG B:250 , HIS B:251 , ARG B:254binding site for residue SO4 B 401
10AD1SOFTWARETHR B:69 , ALA B:70 , GLY B:71 , ASN B:72 , THR B:73 , GLN B:142 , HOH B:554binding site for residue SO4 B 402
11AD2SOFTWAREHIS A:85 , ILE B:20 , GLU B:21 , VAL B:22 , HIS B:25 , HOH B:514binding site for residue GOL B 403
12AD3SOFTWAREARG B:56 , ARG B:58binding site for residue GOL B 404
13AD4SOFTWAREHIS B:85 , ARG B:254 , HOH B:561 , ALA C:132binding site for residue GOL B 405
14AD5SOFTWARETHR B:169 , PRO B:279 , ALA B:280 , SER B:282binding site for residue GOL B 406
15AD6SOFTWAREARG C:250 , HIS C:251 , ARG C:254binding site for residue SO4 C 401
16AD7SOFTWARETHR C:69 , ALA C:70 , GLY C:71 , ASN C:72 , THR C:73 , GLN C:142 , HOH C:535 , HOH C:541binding site for residue SO4 C 402
17AD8SOFTWARESER B:135 , ASN B:136 , LYS C:62 , ASN C:136 , SO4 C:404 , HOH C:526 , HOH C:539binding site for residue SO4 C 403
18AD9SOFTWARELYS B:62 , ASN B:136 , SER C:135 , ASN C:136 , SO4 C:403 , HOH C:536binding site for residue SO4 C 404
19AE1SOFTWAREHIS C:154 , THR C:155 , GLU C:159 , HOH C:530binding site for residue GOL C 405
20AE2SOFTWARELEU C:54 , ALA C:61 , HIS C:84 , HOH C:556 , ASN D:24 , THR D:276binding site for residue GOL C 406
21AE3SOFTWARETHR C:169 , ALA C:280 , ASN C:281 , SER C:282binding site for residue GOL C 407
22AE4SOFTWARETHR D:69 , ALA D:70 , GLY D:71 , ASN D:72 , THR D:73 , GLN D:142 , HOH D:514binding site for residue SO4 D 401
23AE5SOFTWAREARG D:250 , HIS D:251 , ARG D:254binding site for residue SO4 D 402
24AE6SOFTWAREHIS C:85 , ILE D:20 , GLU D:21 , VAL D:22 , HIS D:25 , HOH D:512binding site for residue GOL D 403
25AE7SOFTWAREPRO A:165 , HIS A:283 , LEU D:2 , GLN D:4 , GLU D:8binding site for residue GOL D 404
26AE8SOFTWARETHR D:169 , PRO D:279 , ALA D:280 , SER D:282 , HOH D:518 , HOH D:548binding site for residue GOL D 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B1H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B1H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B1H)

(-) Exons   (0, 0)

(no "Exon" information available for 5B1H)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhh....eee....hhhhheeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee..hhhhh................hhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......eeeeee...hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b1h A   1 MLIQHVQELIGHTPLMALPIEVPNHSHIYAKLEMFNPGGSIkDRLGAYLIEDGLQRGRVNAKTTIIEPTAGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEEGIKGAIRKAEALAATISNSYVPMQFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGSGGTFAGVAAYLQAQDSATKAVVVEPEGSILNGGPAHAHRTEGIGVEFIPPFFDQVRIDQTLTIADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLPANSHIVTIFPDSSERYLSQKIYTK 303
                                    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       300   
                                                                    42-LLP                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....eee....hhhhheeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......................hhhhhhh...eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b1h B   1 MLIQHVQELIGHTPLMALPIEVPNHSHIYAKLEMFNPGGSIkDRLGAYLIEDGLQRGRVNAKTTIIEPTAGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEEGIKGAIRKAEALAATISNSYVPMQFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGSGGTFAGVAAYLQAQDSATKAVVVEPEGSILNGGPAHAHRTEGIGVEFIPPFFDQVRIDQTLTIADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLPANSHIVTIFPDSSERYLSQKIYTK 303
                                    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       300   
                                                                    42-LLP                                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhh....eee....hhhhheeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeee........................hhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b1h C   1 MLIQHVQELIGHTPLMALPIEVPNHSHIYAKLEMFNPGGSIkDRLGAYLIEDGLQRGRVNAKTTIIEPTAGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEEGIKGAIRKAEALAATISNSYVPMQFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGSGGTFAGVAAYLQAQDSATKAVVVEPEGSILNGGPAHAHRTEGIGVEFIPPFFDQVRIDQTLTIADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLPANSHIVTIFPDSSERYLSQKIYTK 303
                                    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       300   
                                                                    42-LLP                                                                                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....eee....hhhhheeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeee........................hhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b1h D   1 MLIQHVQELIGHTPLMALPIEVPNHSHIYAKLEMFNPGGSIkDRLGAYLIEDGLQRGRVNAKTTIIEPTAGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEEGIKGAIRKAEALAATISNSYVPMQFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGSGGTFAGVAAYLQAQDSATKAVVVEPEGSILNGGPAHAHRTEGIGVEFIPPFFDQVRIDQTLTIADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLPANSHIVTIFPDSSERYLSQKIYTK 303
                                    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       300   
                                                                    42-LLP
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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 '|'

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(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5B1H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B1H)

(-) Gene Ontology  (3, 3)

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