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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE SYNTHASE DOUBLE MUTANT C195S-Y202C
 
Authors :  C. Pozzi, S. Mangani
Date :  16 Dec 13  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Dimer-Dimer Interface Modification, Active Conformation, Methyltransferase, Nucleotide Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ferrari, S. Mangani, C. Pozzi, M. P. Costi
Tethering The Dimer-Dimer Interface Of Human Thymidylate Synthase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B, C
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-80L
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OK/SW-CL.29, TS, TYMS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TS, TSASE
 
Molecule 2 - THYMIDYLATE SYNTHASE
    Chains: D
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-80L
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OK/SW-CL.29, TS, TYMS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TS, TSASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2CME8Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3EDO5Ligand/Ion1,2-ETHANEDIOL
4SCH5Mod. Amino AcidS-METHYL-THIO-CYSTEINE
5SO48Ligand/IonSULFATE ION
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CME4Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3EDO3Ligand/Ion1,2-ETHANEDIOL
4SCH2Mod. Amino AcidS-METHYL-THIO-CYSTEINE
5SO45Ligand/IonSULFATE ION
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CME4Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4SCH3Mod. Amino AcidS-METHYL-THIO-CYSTEINE
5SO43Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:175 , ARG A:176 , PRO C:193 , ARG C:215BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWAREARG A:274BINDING SITE FOR RESIDUE CL A 404
03AC3SOFTWAREARG A:163 , VAL A:164 , THR A:167 , ARG A:176 , ILE A:178 , HOH A:519BINDING SITE FOR RESIDUE EDO A 405
04AC4SOFTWARELEU A:89 , ILE A:92 , ILE A:288 , ASP A:289 , PHE A:291BINDING SITE FOR RESIDUE EDO A 406
05AC5SOFTWAREARG A:78 , PRO A:305 , THR A:306 , ARG B:78 , PRO B:305 , THR B:306BINDING SITE FOR RESIDUE SO4 A 407
06AC6SOFTWAREPRO A:193 , ARG A:215 , ARG C:175 , ARG C:176BINDING SITE FOR RESIDUE SO4 A 408
07AC7SOFTWAREARG B:175 , ARG B:176 , ARG D:215BINDING SITE FOR RESIDUE SO4 B 401
08AC8SOFTWAREARG B:163 , VAL B:164 , THR B:167 , ARG B:176 , ILE B:178 , HOH B:525BINDING SITE FOR RESIDUE EDO B 402
09AC9SOFTWAREGLU C:272 , ARG C:274 , HIS C:304BINDING SITE FOR RESIDUE SO4 C 401
10BC1SOFTWAREARG C:147 , SER C:151 , ASP C:152BINDING SITE FOR RESIDUE SO4 C 402
11BC2SOFTWAREARG C:163 , VAL C:164 , ILE C:178 , HOH C:508BINDING SITE FOR RESIDUE EDO C 403
12BC3SOFTWAREARG B:50 , ARG D:78 , PRO D:305 , THR D:306 , HOH D:528BINDING SITE FOR RESIDUE SO4 D 401
13BC4SOFTWAREARG B:50 , PRO B:193 , ARG B:215 , ARG D:175 , ARG D:176 , HOH D:534 , HOH D:544BINDING SITE FOR RESIDUE SO4 D 402
14BC5SOFTWAREARG D:163 , VAL D:164 , THR D:167 , ILE D:178BINDING SITE FOR RESIDUE EDO D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O1X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O1X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O1X)

(-) Exons   (0, 0)

(no "Exon" information available for 4O1X)

(-) 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:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhh.............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o1x A  24 PRPPHGELQYLGQIQHILRcGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPSHALcQFcVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEM 311
                                    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        
                                              43-SCH                                                                                                                                                     199-CME                                                                                                            
                                                                                                                                                                                                            202-CME                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhee........eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeee...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o1x B  24 PRPPHGELQYLGQIQHILRcGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPSHALcQFcVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEM 311
                                    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        
                                              43-SCH                                                                                                                                                     199-CME                                                                                                            
                                                                                                                                                                                                            202-CME                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhh.............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o1x C  26 PPHGELQYLGQIQHILRcGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPSHALcQFcVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEM 311
                                    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      
                                            43-SCH                                                                                                                                                     199-CME                                                                                                            
                                                                                                                                                                                                          202-CME                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhheee...eeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhh.............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o1x D  29 GELQYLGQIQHILRcGVRKDDGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMcAWNPRDLPLMALPPSHALcQFcVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKME 310
                                    38    |   48||      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        
                                         43-SCH49|                                                                                                                           180-SCH            199-CME                                                                                                           
                                                54                                                                                                                                                 202-CME
   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  (0, 0)

(no "SCOP Domain" information available for 4O1X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O1X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O1X)

(-) Gene Ontology  (52, 52)

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  4o1x
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  TYSY_HUMAN | P04818
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  2.1.1.45
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 Related Entries

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

UniProtKB/Swiss-Prot
        TYSY_HUMAN | P04818: 1hvy 1hw3 1hw4 1hzw 1i00 1ju6 1juj 1ypv 2onb 2rd8 2rda 3eaw 3ebu 3ed7 3edw 3ef9 3egy 3ehi 3ejl 3gg5 3gh0 3gh2 3h9k 3hb8 3n5e 3n5g 3ob7 4e28 4fgt 4g2o 4g6w 4gd7 4gyh 4h1i 4jef 4kpw 4o1u 4up1 5hs3 5wrn 5x4w 5x4x 5x4y 5x5a 5x5d 5x5q 5x66 5x67 5x69

(-) Related Entries Specified in the PDB File

4o1u