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(-) Description

Title :  ENGINEERED TRYPTOPHAN SYNTHASE B-SUBUNIT FROM PYROCOCCUS FURIOSUS, PFTRPB2B9, WITH SER BOUND
 
Authors :  A. R. Buller, P. Van Roye
Date :  26 Apr 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Plp, Non-Canonical Amino Acid, Directed Evolution, Allostery, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Buller, P. Van Roye
Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, Pftrpb2B9, With Ser Bound
To Be Published
PubMed: search

(-) 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 BL21(DE3)
    Expression System Taxid: 469008
    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, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
10JO1Ligand/Ion2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOICACID
2NA7Ligand/IonSODIUM ION
3PLS3Ligand/Ion[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
10JO-1Ligand/Ion2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOICACID
2NA-1Ligand/IonSODIUM ION
3PLS2Ligand/Ion[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
10JO1Ligand/Ion2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOICACID
2NA-1Ligand/IonSODIUM ION
3PLS1Ligand/Ion[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:81 , LYS A:82 , THR A:105 , GLY A:106 , ALA A:107 , GLY A:108 , GLN A:109 , HIS A:110 , SER A:185 , GLY A:227 , GLY A:228 , GLY A:229 , SER A:230 , ASN A:231 , GLY A:298 , ASP A:300 , GLU A:345 , SER A:371 , HOH A:535 , HOH A:569 , HOH A:605binding site for residue PLS A 401
02AC2SOFTWAREGLY A:227 , SER A:263 , SER A:265 , TYR A:301 , GLY A:303 , HOH A:570 , HOH A:585binding site for residue NA A 402
03AC3SOFTWAREGLY A:48 , PRO A:50 , HOH A:636 , GLY B:48 , PRO B:50 , HOH B:627binding site for residue NA A 403
04AC4SOFTWAREHIS B:81 , LYS B:82 , THR B:105 , GLY B:106 , ALA B:107 , GLY B:108 , GLN B:109 , HIS B:110 , SER B:185 , GLY B:227 , GLY B:228 , GLY B:229 , SER B:230 , ASN B:231 , GLY B:298 , ASP B:300 , GLU B:345 , SER B:371 , HOH B:534 , HOH B:573binding site for residue PLS B 401
05AC5SOFTWARESER B:263 , SER B:265 , TYR B:301 , GLY B:303 , HOH B:589 , HOH B:601binding site for residue NA B 402
06AC6SOFTWAREHIS C:81 , LYS C:82 , THR C:105 , GLY C:106 , ALA C:107 , GLY C:108 , GLN C:109 , HIS C:110 , SER C:185 , GLY C:227 , GLY C:228 , GLY C:229 , SER C:230 , ASN C:231 , GLY C:298 , ASP C:300 , GLU C:345 , SER C:371 , HOH C:534 , HOH C:551 , HOH C:579binding site for residue PLS C 401
07AC7SOFTWARESER C:263 , SER C:265 , TYR C:301 , GLY C:303 , HOH C:556 , HOH C:576binding site for residue NA C 402
08AC8SOFTWARETRP A:2 , GLY A:4 , GLU A:5 , HOH A:516 , GLN C:283 , GLY C:287 , HOH C:631binding site for residue NA C 403
09AC9SOFTWAREGLY C:48 , PRO C:50 , HOH C:634 , GLY D:48 , PRO D:50 , HOH D:638binding site for residue NA C 404
10AD1SOFTWARESER D:263 , SER D:265 , TYR D:301 , GLY D:303 , HOH D:570 , HOH D:605binding site for residue NA D 401
11AD2SOFTWAREHIS D:81 , LYS D:82 , THR D:105 , GLY D:106 , ALA D:107 , GLY D:108 , GLN D:109 , HIS D:110 , SER D:185 , CYS D:225 , GLY D:227 , GLY D:228 , GLY D:229 , SER D:230 , ASN D:231 , GLY D:298 , GLU D:345 , SER D:371 , HOH D:514 , HOH D:545binding site for residue 0JO D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5VM5)

(-) 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 5VM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VM5)

(-) Exons   (0, 0)

(no "Exon" information available for 5VM5)

(-) 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..eeeee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee.eeeeee.......................hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vm5 A   1 MWFGEFGGQYVPETLVGPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKVYLKREDLVHGGAHKTNNAIGQALLAKLMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVSHGMLSYFLQDEEGQIKPSHSIAPGLDYPGVGPEHAYLKKIQRAEYVAVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKA 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    


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..eeeeee.hhh....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee..eeeee....................hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vm5 B   1 MWFGEFGGQYVPETLVGPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKVYLKREDLVHGGAHKTNNAIGQALLAKLMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVSHGMLSYFLQGQIKPSHSIAPGLDYPGVGPEHAYLKKIQRAEYVAVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKAS 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  
                                                                                                                                                                                                                                                                                                                    283|                                                                                                  
                                                                                                                                                                                                                                                                                                                     287                                                                                                  


Chain C 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....hhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.........hhhhhh.eeee..eeee........................hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vm5 C   1 MWFGEFGGQYVPETLVGPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKVYLKREDLVHGGAHKTNNAIGQALLAKLMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVSHGMLSYFLQDEEGQIKPSHSIAPGLDYPGVGPEHAYLKKIQRAEYVAVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLK 383
                                    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   


Chain D 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...eeeeee..hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee..eeeee............hhhhh....hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vm5 D   1 MWFGEFGGQYVPETLVGPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKVYLKREDLVHGGAHKTNNAIGQALLAKLMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVSHGMLSYFLQDGQIKPSHSIAPGLDYPGVGPEHAYLKKIQRAEYVAVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKAS 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   
                                                                                                                                                                                                                                                                                                                     284|                                                                                                  
                                                                                                                                                                                                                                                                                                                      287
   Legend:   → Mismatch (orange background)
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  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 5VM5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VM5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VM5)

(-) 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)

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        TRPB1_PYRFU | Q8U093: 1v8z 1wdw 5dvz 5dw0 5dw3 5e0k 5ixj 5t6m

(-) Related Entries Specified in the PDB File

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