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(-) Description

Title :  TRYPTOPHAN SYNTHASE BETA-SUBUNIT FROM PYROCOCCUS FURIOSUS WITH PRODUCT L-TRYPTOPHAN NON-COVALENTLY BOUND IN THE ACTIVE SITE
 
Authors :  A. R. Buller, F. H. Arnold
Date :  22 Sep 15  (Deposition) - 11 Nov 15  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Tryptophan Synthase, Plp, External Aldimine, Substrate Bound, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Buller, S. Brinkmann-Chen, D. K. Romney, M. Herger, J. Murciano-Calles, F. H. Arnold
Directed Evolution Of The Tryptophan Synthase Beta-Subunit For Stand-Alone Function Recapitulates Allosteric Activation.
Proc. Natl. Acad. Sci. Usa V. 112 14599 2015
PubMed-ID: 26553994  |  Reference-DOI: 10.1073/PNAS.1516401112

(-) Compounds

Molecule 1 - TRYPTOPHAN SYNTHASE BETA CHAIN 1
    Chains: A, B, C, D
    EC Number: 4.2.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: TRPB1, PF1706
    Organism Scientific: PYROCOCCUS FURIOSUS (STRAIN ATCC 43587 / DSM 3638 / JCM 8422 / VC1)
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1

 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  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1LLP4Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
2NA4Ligand/IonSODIUM ION
3PO42Ligand/IonPHOSPHATE ION
4TRP4Mod. Amino AcidTRYPTOPHAN
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
2NA-1Ligand/IonSODIUM ION
3PO4-1Ligand/IonPHOSPHATE ION
4TRP2Mod. Amino AcidTRYPTOPHAN
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
2NA-1Ligand/IonSODIUM ION
3PO42Ligand/IonPHOSPHATE ION
4TRP2Mod. Amino AcidTRYPTOPHAN

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:263 , SER A:265 , TYR A:301 , GLY A:303 , HOH A:503 , HOH A:555binding site for residue NA A 401
2AC2SOFTWAREGLY B:227 , SER B:263 , SER B:265 , TYR B:301 , GLY B:303 , HOH B:508 , HOH B:543binding site for residue NA B 401
3AC3SOFTWARESER C:263 , SER C:265 , TYR C:301 , GLY C:303 , HOH C:502 , HOH C:527binding site for residue NA C 401
4AC4SOFTWARELLP C:82 , THR C:105 , GLY C:106 , ALA C:107 , GLY C:108 , GLN C:109 , HIS C:110binding site for residue PO4 C 403
5AC5SOFTWARESER D:263 , SER D:265 , TYR D:301 , GLY D:303 , HOH D:511 , HOH D:538binding site for residue NA D 401
6AC6SOFTWARELLP D:82 , THR D:105 , GLY D:106 , ALA D:107 , GLY D:108 , HIS D:110binding site for residue PO4 D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DW3)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Arg A:49 -Pro A:50
2His A:190 -Pro A:191
3Arg B:49 -Pro B:50
4His B:190 -Pro B:191
5Arg C:49 -Pro C:50
6His C:190 -Pro C:191
7Arg D:49 -Pro D:50
8His D:190 -Pro D:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DW3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DW3)

(-) Exons   (0, 0)

(no "Exon" information available for 5DW3)

(-) 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:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee..eeeee.............hhhhh....hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dw3 A   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKV 384
                                    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   ||  291       301       311       321       331       341       351       361       371       381   
                                                                                                            82-LLP                                                                                                                                                                                                   284|                                                                                                  
                                                                                                                                                                                                                                                                                                                      286                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee..eeeee.............hhhhh....hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dw3 B   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVSGN 387
                                    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   ||  291       301       311       321       331       341       351       361       371       381      
                                                                                                            82-LLP                                                                                                                                                                                                   284|                                                                                                     
                                                                                                                                                                                                                                                                                                                      286                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..ee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeee.hhhh....hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee..eeeee.............hhhhh....hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dw3 C   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVS 385
                                    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   ||  291       301       311       321       331       341       351       361       371       381    
                                                                                                            82-LLP                                                                                                                                                                                                   284|                                                                                                   
                                                                                                                                                                                                                                                                                                                      286                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..ee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee..eeeee.............hhhhh....hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dw3 D   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVS 385
                                    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   ||  291       301       311       321       331       341       351       361       371       381    
                                                                                                            82-LLP                                                                                                                                                                                                   284|                                                                                                   
                                                                                                                                                                                                                                                                                                                      286
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  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 5DW3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DW3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DW3)

(-) Gene Ontology  (6, 6)

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  5dw3
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  TRPB1_PYRFU | Q8U093
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  4.2.1.20
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRPB1_PYRFU | Q8U093: 1v8z 1wdw 5dvz 5dw0 5e0k 5ixj 5t6m 5vm5

(-) Related Entries Specified in the PDB File

5dvz 5dw0 5e0k