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(-) Description

Title :  HOLO TRPB FROM PYROCOCCUS FURIOSUS
 
Authors :  A. R. Buller, F. H. Arnold
Date :  21 Sep 15  (Deposition) - 03 Feb 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Type Ii Plp Enzyme, Tryptophan Biosynthesis, Ec 4. 2. 1. 20, 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 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  (3, 12)

Asymmetric Unit (3, 12)
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
3PO44Ligand/IonPHOSPHATE ION
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
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (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
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:263 , SER A:265 , TYR A:301 , GLY A:303 , HOH A:601 , HOH A:613binding site for residue NA A 401
2AC2SOFTWARETHR A:105 , GLY A:106 , ALA A:107 , GLY A:108 , GLN A:109 , HIS A:110 , HOH A:528 , HOH A:566 , HOH A:612binding site for residue PO4 A 402
3AC3SOFTWARESER B:263 , SER B:265 , TYR B:301 , GLY B:303 , HOH B:536 , HOH B:614binding site for residue NA B 401
4AC4SOFTWARELLP B:82 , THR B:105 , GLY B:106 , ALA B:107 , GLY B:108 , GLN B:109 , HIS B:110 , HOH B:585 , HOH B:609binding site for residue PO4 B 402
5AC5SOFTWARESER C:263 , SER C:265 , TYR C:301 , GLY C:303 , HOH C:544 , HOH C:582binding site for residue NA C 401
6AC6SOFTWARETHR C:105 , GLY C:106 , ALA C:107 , GLY C:108 , GLN C:109 , HIS C:110 , HOH C:620 , HOH C:626binding site for residue PO4 C 402
7AC7SOFTWARESER D:263 , SER D:265 , TYR D:301 , GLY D:303 , HOH D:577 , HOH D:623binding site for residue NA D 401
8AC8SOFTWARELLP D:82 , THR D:105 , GLY D:106 , ALA D:107 , GLY D:108 , GLN D:109 , HIS D:110 , ASP D:300 , HOH D:614 , HOH D:648binding site for residue PO4 D 402

(-) SS Bonds  (0, 0)

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

(-) 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 5DVZ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DVZ)

(-) 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:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..ee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeee.hhhh....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.........hhhhhheeeee..eeeee..............hhhhh....hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dvz A   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKV 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       290       300       310       320       330       340       350       360       370       380    
                                                                                                            82-LLP                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeee.hhhh....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee..eeeee............hhhhh....hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dvz B   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKV 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   ||  292       302       312       322       332       342       352       362       372       382  
                                                                                                            82-LLP                                                                                                                                                                                                   284|                                                                                                 
                                                                                                                                                                                                                                                                                                                      287                                                                                                 


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..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.........hhhhhheeeee..eeeee............hhhhh....hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dvz C   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVSG 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   ||  292       302       312       322       332       342       352       362       372       382    
                                                                                                            82-LLP                                                                                                                                                                                                   284|                                                                                                   
                                                                                                                                                                                                                                                                                                                      287                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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.......................hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dvz D   1 MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHkTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVS 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       290       300       310       320       330       340       350       360       370       380     
                                                                                                            82-LLP
   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 5DVZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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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 5dw0 5dw3 5e0k 5ixj 5t6m 5vm5

(-) Related Entries Specified in the PDB File

5dw0 5dw3