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(-) Description

Title :  STRUCTURE OF THE TRYPTOPHAN SYNTHASE B-SUBUNIT FROM PYROCCUS FURIOSUS WITH B-METHYLTRYPTOPHAN NON-COVALENTLY BOUND
 
Authors :  A. R. Buller, P. Van Roye, F. H. Arnold
Date :  01 Sep 16  (Deposition) - 21 Dec 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Tryptophan Synthase, Plp, Non-Canonical Amino Acid, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Buller, P. Van Roye, J. Murciano-Calles, F. H. Arnold
Tryptophan Synthase Uses An Atypical Mechanism To Achieve Substrate Specificity.
Biochemistry V. 55 7043 2016
PubMed-ID: 27935677  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B01127

(-) 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 Taxid: 562
    Gene: TRPB1, PF1706
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 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, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
178U3Ligand/Ion(BETAS)-BETA-METHYL-L-TRYPTOPHAN
2LLP4Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3NA4Ligand/IonSODIUM ION
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
178U1Ligand/Ion(BETAS)-BETA-METHYL-L-TRYPTOPHAN
2LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3NA-1Ligand/IonSODIUM ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
178U2Ligand/Ion(BETAS)-BETA-METHYL-L-TRYPTOPHAN
2LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
3NA-1Ligand/IonSODIUM ION
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:263 , SER A:265 , TYR A:301 , GLY A:303 , HOH A:548 , HOH A:551binding site for residue NA A 401
2AC2SOFTWARELLP A:82 , THR A:105 , GLY A:106 , ALA A:107 , GLY A:108 , GLN A:109 , HIS A:110 , HOH A:502binding site for residue PO4 A 402
3AC3SOFTWAREGLY B:227 , SER B:263 , SER B:265 , TYR B:301 , GLY B:303 , HOH B:519 , HOH B:549binding site for residue NA B 401
4AC4SOFTWARELLP B:82 , GLU B:104 , THR B:105 , GLY B:106 , ALA B:107 , GLY B:108 , GLN B:109 , HIS B:110 , LEU B:161 , GLY B:298 , TYR B:301 , HOH B:523binding site for residue 78U B 402
5AC5SOFTWAREGLY C:227 , SER C:263 , SER C:265 , TYR C:301 , GLY C:303 , HOH C:524 , HOH C:538binding site for residue NA C 401
6AC6SOFTWARELLP C:82 , GLU C:104 , THR C:105 , GLY C:106 , ALA C:107 , GLN C:109 , HIS C:110 , LEU C:161 , VAL C:187 , GLY C:298 , TYR C:301 , HOH C:508binding site for residue 78U C 402
7AC7SOFTWAREGLY D:227 , SER D:263 , SER D:265 , TYR D:301 , GLY D:303 , HOH D:536binding site for residue NA D 401
8AC8SOFTWARETHR D:105 , GLY D:106 , ALA D:107 , GLN D:109 , HIS D:110 , HOH D:548binding site for residue PO4 D 402
9AC9SOFTWAREGLU D:104 , LEU D:169 , TYR D:181 , ILE D:183 , PRO D:189 , HIS D:275 , TYR D:301 , HOH D:525 , HOH D:542binding site for residue 78U D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T6M)

(-) 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 5T6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T6M)

(-) Exons   (0, 0)

(no "Exon" information available for 5T6M)

(-) 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....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.........hhhhhheeeee..eeeee............hhhhh....hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t6m A   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVS 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   ||  292       302       312       322       332       342       352       362       372       382   
                                                                                                            82-LLP                                                                                                                                                                                                   284|                                                                                                  
                                                                                                                                                                                                                                                                                                                      287                                                                                                  


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....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee..eeeee..............hhhhh....hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t6m B   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVSG 386
                                    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       310       320       330       340       350       360       370       380      
                                                                                                            82-LLP                                                                                                                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeee.hhhh....hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee..eeeee..............hhhhh....hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t6m C   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVSGNVLEH 391
                                    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       310       320       330       340       350       360       370       380       390 
                                                                                                            82-LLP                                                                                                                                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeee...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
                 5t6m D   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVS 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   ||  293       303       313       323       333       343       353       363       373       383  
                                                                                                            82-LLP                                                                                                                                                                                                   284|                                                                                                 
                                                                                                                                                                                                                                                                                                                      288
   Legend:   → Mismatch (orange background)
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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 5T6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T6M)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  TRPB1_PYRFU | Q8U093
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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 5dw3 5e0k 5ixj 5vm5

(-) Related Entries Specified in the PDB File

5dvz
5dw3 SAME PROTEIN, BUT WITH B-METRP BOUND IN THE ACTIVE SITE.