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(-) Description

Title :  CRYSTAL STRUCTURE OF HYDROGEN SULFIDE-PRODUCING ENZYME (FN1055) FROM FUSOBACTERIUM NUCLEATUM: LYSINE-DIMETHYLATED FORM
 
Authors :  Y. Kezuka, Y. Yoshida, T. Nonaka
Date :  22 Apr 16  (Deposition) - 26 Apr 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Pyridoxal 5'-Phosphate Dependent Enzyme, Internal Aldimine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kezuka, Y. Yoshida, T. Nonaka
Crystal Structure Of Hydrogen Sulfide-Producing Enzyme (Fn1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYSTEINE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.5.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FN1055
    Organism Scientific: FUSOBACTERIUM NUCLEATUM SUBSP. NUCLEATUM STRAIN ATCC 25586
    Organism Taxid: 190304
    Strain: ATCC 25586

 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  (3, 150)

Asymmetric Unit (3, 150)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MLY142Mod. Amino AcidN-DIMETHYL-LYSINE
3PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 72)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MLY70Mod. Amino AcidN-DIMETHYL-LYSINE
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 74)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MLY72Mod. Amino AcidN-DIMETHYL-LYSINE
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:46 , ASN A:76 , GLY A:182 , VAL A:183 , GLY A:184 , THR A:185 , GLY A:186 , THR A:188 , GLY A:229 , ILE A:230 , SER A:272 , PRO A:298 , ASP A:299 , TYR A:304 , HOH A:515 , HOH A:529 , HOH A:561 , HOH A:570binding site for residue PLP A 401
2AC2SOFTWARELYS A:46 , THR A:73 , SER A:74 , THR A:77 , GLN A:147binding site for residue CL A 402
3AC3SOFTWARELYS C:46 , THR C:73 , SER C:74 , THR C:77 , GLN C:147binding site for residue CL C 402
4AC4SOFTWARECYS C:206 , ASN C:246 , MLY C:286binding site for residue CL C 403
5AC5SOFTWARELYS D:46 , THR D:73 , SER D:74 , THR D:77 , GLN D:147binding site for residue CL D 402
6AC6SOFTWARESER B:44 , ILE B:45 , ASP B:47 , ARG B:48 , MET B:49 , ALA B:50 , ASN B:76 , THR B:77 , ALA B:80 , VAL B:183 , GLY B:184 , THR B:185 , GLY B:186 , GLY B:187 , THR B:188 , GLY B:229 , ILE B:230 , SER B:272 , PRO B:298 , ASP B:299 , HOH B:512 , HOH B:517 , HOH B:547binding site for Di-peptide PLP B 401 and LYS B 46
7AC7SOFTWARESER C:44 , ILE C:45 , ASP C:47 , ARG C:48 , MET C:49 , ALA C:50 , ASN C:76 , THR C:77 , GLY C:182 , VAL C:183 , GLY C:184 , THR C:185 , GLY C:186 , GLY C:187 , THR C:188 , GLY C:229 , ILE C:230 , SER C:272 , PRO C:298 , ASP C:299 , TYR C:304 , CL C:402 , HOH C:509 , HOH C:532 , HOH C:550 , HOH C:555binding site for Di-peptide PLP C 401 and LYS C 46
8AC8SOFTWARESER D:44 , ILE D:45 , ASP D:47 , ARG D:48 , MET D:49 , ALA D:50 , ASN D:76 , THR D:77 , ALA D:80 , GLY D:182 , VAL D:183 , GLY D:184 , THR D:185 , GLY D:186 , GLY D:187 , THR D:188 , GLY D:229 , ILE D:230 , SER D:272 , PRO D:298 , ASP D:299 , TYR D:304 , CL D:402 , HOH D:505 , HOH D:519 , HOH D:527 , HOH D:544binding site for Di-peptide PLP D 401 and LYS D 46

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B54)

(-) Cis Peptide Bonds  (4, 5)

Asymmetric Unit
No.Residues
1Mly B:26 -Gly B:27
2Arg B:120 -Mly B:121
3Gly B:124 -Phe B:125
4Mly C:26 -Gly C:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B54)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B54)

(-) Exons   (0, 0)

(no "Exon" information available for 5B54)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeeeee..eeeeeeeee........hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhh....................hhhhh...eeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....eeeee...hhhhh.hhhhh.......hhhh.eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b54 A   6 MkYLENLVGkTPMLELIFDYkGEERRIFVkNESYNLTGSIKDRMAFYTLkkAYEkNEIkkGAPIVEATSGNTGIAFSAMGAILGHPVIIYMPDWMSEERkSLIRSFGAkIILVSRkEGGFLGSIEkTkEFAkNNPDTYLPSQFSNLYNSEAHYYGIGLEIVNEMkSLNLNIDGFVAGVGTGGTVMGIGkRIkENFSNAkICPLEPLNSPTLSTGYkVAkHRIEGISDEFIPDLVkLDkLDNVVSVDDGDAIVMAQkLAkCGLGVGISSGANFIGALMLQNkLGkDSVIVTVFPDDNkkYLSTDLMREEkVkEDFLSkDITLkEIkNVLRVI 336
                             |      15        25|       35        45        55|   |   65        75        85        95       105       115     | 125     | 135 |     145       155       165    |  175       185       195 |     205       215     | 225       235    |  245       255     | 265       275       285|  |   295      |305       315|     |325 |  |  335 
                             |      15-MLY     26-MLY   35-MLY              55-MLY|   ||                                     105-MLY  114-MLY  |       131-MLY |                              170-MLY                 194-MLY     |              221-MLY            240-MLY              261-MLY                  286-MLY         302-MLY     314-MLY   |    |  |      
                             7-MLY                                           56-MLY   ||                                                     121-MLY     133-MLY                                                         197-MLY  |                 224-MLY            243-MLY              264-MLY                  289-MLY       303-MLY      316-MLY |    |  |      
                                                                                 60-MLY|                                                                     137-MLY                                                            204-MLY                                                                                                               322-MLY|  |      
                                                                                     64-MLY                                                                                                                                                                                                                                                                327-MLY     
                                                                                      65-MLY                                                                                                                                                                                                                                                                  330-MLY  


Chain B from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....eeeeeeee..eeeeeeeee........hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhh....................hhhhh...eeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....eeeee...hhhhh.hhhhh........hhh.eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5b54 B   0 GSEQkkMkYLENLVGkTPMLELIFDYkGEERRIFVkNESYNLTGSIKDRMAFYTLkkAYEkNEIkkGAPIVEATSGNTGIAFSAMGAILGHPVIIYMPDWMSEERkSLIRSFGAkIILVSRkEGGFLGSIEkTkEFAkNNPDTYLPSQFSNLYNSEAHYYGIGLEIVNEMkSLNLNIDGFVAGVGTGGTVMGIGkRIkENFSNAkICPLEPLNSPTLSTGYkVAkHRIEGISDEFIPDLVkLDkLDNVVSVDDGDAIVMAQkLAkCGLGVGISSGANFIGALMLQNkLGkDSVIVTVFPDDNkkYLSTDLMREEkVkEDFLSkDITLkEIkNVLRV 335
                                || | 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  |    329|     
                                4-MLY     15-MLY     26-MLY   35-MLY              55-MLY|   ||                                     105-MLY  114-MLY  |       131-MLY |                              170-MLY                 194-MLY     |              221-MLY            240-MLY              261-MLY                  286-MLY         302-MLY     314-MLY   |    |  |     
                                 5-MLY                                             56-MLY   ||                                                     121-MLY     133-MLY                                                         197-MLY  |                 224-MLY            243-MLY              264-MLY                  289-MLY       303-MLY      316-MLY |    |  |     
                                   7-MLY                                               60-MLY|                                                                     137-MLY                                                            204-MLY                                                                                                               322-MLY|  |     
                                                                                           64-MLY                                                                                                                                                                                                                                                                327-MLY    
                                                                                            65-MLY                                                                                                                                                                                                                                                                  330-MLY 


Chain C from PDB  Type:PROTEIN  Length:333
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....eeeeeeee..eeeeeeeee........hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhh....................hhhhh...eeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....eeeee...hhhhh.hhhhh........hhh.eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b54 C   4 kkMkYLENLVGkTPMLELIFDYkGEERRIFVkNESYNLTGSIKDRMAFYTLkkAYEkNEIkkGAPIVEATSGNTGIAFSAMGAILGHPVIIYMPDWMSEERkSLIRSFGAkIILVSRkEGGFLGSIEkTkEFAkNNPDTYLPSQFSNLYNSEAHYYGIGLEIVNEMkSLNLNIDGFVAGVGTGGTVMGIGkRIkENFSNAkICPLEPLNSPTLSTGYkVAkHRIEGISDEFIPDLVkLDkLDNVVSVDDGDAIVMAQkLAkCGLGVGISSGANFIGALMLQNkLGkDSVIVTVFPDDNkkYLSTDLMREEkVkEDFLSkDITLkEIkNVLRVI 336
                            || |    13 |      23  |     33 |      43        53 ||   | 63||      73        83        93       103 |     113|      123       133   |   143       153       163      |173       183       193|  |   203|      213       223|      233      |243       253       263|      273       283  |  | 293       303       313| |    323   |  |333   
                            4-MLY     15-MLY     26-MLY   35-MLY              55-MLY|   ||                                     105-MLY  114-MLY  |       131-MLY |                              170-MLY                 194-MLY     |              221-MLY            240-MLY              261-MLY                  286-MLY         302-MLY     314-MLY   |    |  |      
                             5-MLY                                             56-MLY   ||                                                     121-MLY     133-MLY                                                         197-MLY  |                 224-MLY            243-MLY              264-MLY                  289-MLY       303-MLY      316-MLY |    |  |      
                               7-MLY                                               60-MLY|                                                                     137-MLY                                                            204-MLY                                                                                                               322-MLY|  |      
                                                                                       64-MLY                                                                                                                                                                                                                                                                327-MLY     
                                                                                        65-MLY                                                                                                                                                                                                                                                                  330-MLY  


Chain D from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....eeeeeeee..eeeeeeeee........hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhh....................hhhhh...eeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....eeeee..hhhhhh.hhhhh........hhh.eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b54 D   4 kkMkYLENLVGkTPMLELIFDYkGEERRIFVkNESYNLTGSIKDRMAFYTLkkAYEkNEIkkGAPIVEATSGNTGIAFSAMGAILGHPVIIYMPDWMSEERkSLIRSFGAkIILVSRkEGGFLGSIEkTkEFAkNNPDTYLPSQFSNLYNSEAHYYGIGLEIVNEMkSLNLNIDGFVAGVGTGGTVMGIGkRIkENFSNAkICPLEPLNSPTLSTGYkVAkHRIEGISDEFIPDLVkLDkLDNVVSVDDGDAIVMAQkLAkCGLGVGISSGANFIGALMLQNkLGkDSVIVTVFPDDNkkYLSTDLMREEkVkEDFLSkDITLkEIkNVLRV 335
                            || |    13 |      23  |     33 |      43        53 ||   | 63||      73        83        93       103 |     113|      123       133   |   143       153       163      |173       183       193|  |   203|      213       223|      233      |243       253       263|      273       283  |  | 293       303       313| |    323   |  |333  
                            4-MLY     15-MLY     26-MLY   35-MLY              55-MLY|   ||                                     105-MLY  114-MLY  |       131-MLY |                              170-MLY                 194-MLY     |              221-MLY            240-MLY              261-MLY                  286-MLY         302-MLY     314-MLY   |    |  |     
                             5-MLY                                             56-MLY   ||                                                     121-MLY     133-MLY                                                         197-MLY  |                 224-MLY            243-MLY              264-MLY                  289-MLY       303-MLY      316-MLY |    |  |     
                               7-MLY                                               60-MLY|                                                                     137-MLY                                                            204-MLY                                                                                                               322-MLY|  |     
                                                                                       64-MLY                                                                                                                                                                                                                                                                327-MLY    
                                                                                        65-MLY                                                                                                                                                                                                                                                                  330-MLY
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5B54)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B54)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B54)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  5b54
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 Related Entries

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

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        Q8REP3_FUSNN | Q8REP3: 5b53 5b55

(-) Related Entries Specified in the PDB File

5b53 5b55