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(-) Description

Title :  RUMINOCOCCUS GNAVUS TRYPTOPHAN DECARBOXYLASE RUMGNA_01526 (ALPHA-FMT)
 
Authors :  J. S. Fraser, A. H. Van Benschoten
Date :  07 Jan 14  (Deposition) - 29 Oct 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Type 1 Plp-Dependent, Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. B. Williams, A. H. Van Benschoten, P. Cimermancic, M. S. Donia, M. Zimmermann, M. Taketani, A. Ishihara, P. C. Kashyap, J. S. Fraser, M. A. Fischbach
Discovery And Characterization Of Gut Microbiota Decarboxylases That Can Produce The Neurotransmitter Tryptamine.
Cell Host Microbe V. 16 495 2014
PubMed-ID: 25263219  |  Reference-DOI: 10.1016/J.CHOM.2014.09.001

(-) Compounds

Molecule 1 - PYRIDOXAL-DEPENDENT DECARBOXYLASE DOMAIN PROTEIN
    Chains: D, C, B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RUMGNA_01526
    Organism Scientific: RUMINOCOCCUS GNAVUS
    Organism Taxid: 411470

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
12SU4Ligand/IonALPHA-(FLUOROMETHYL)-D-TRYPTOPHAN
23SO4Ligand/Ion{5-HYDROXY-4-[(1E)-4-(1H-INDOL-3-YL)-3-OXOBUT-1-EN-1-YL]-6-METHYLPYRIDIN-3-YL}METHYL DIHYDROGEN PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
12SU2Ligand/IonALPHA-(FLUOROMETHYL)-D-TRYPTOPHAN
23SO2Ligand/Ion{5-HYDROXY-4-[(1E)-4-(1H-INDOL-3-YL)-3-OXOBUT-1-EN-1-YL]-6-METHYLPYRIDIN-3-YL}METHYL DIHYDROGEN PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
12SU2Ligand/IonALPHA-(FLUOROMETHYL)-D-TRYPTOPHAN
23SO2Ligand/Ion{5-HYDROXY-4-[(1E)-4-(1H-INDOL-3-YL)-3-OXOBUT-1-EN-1-YL]-6-METHYLPYRIDIN-3-YL}METHYL DIHYDROGEN PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE B:19 , LYS D:40 , PRO D:102 , ALA D:103 , SER D:104 , SER D:105 , PHE D:309 , PRO D:462 , GLU D:463BINDING SITE FOR RESIDUE 2SU D 501
2AC2SOFTWAREHIS B:120 , LEU B:336 , TRP B:349 , THR B:356 , VAL D:99 , GLY D:159 , SER D:160 , HIS D:192 , SER D:194 , THR D:249 , ASP D:274 , ALA D:276 , ASP D:303 , HIS D:305 , LYS D:306BINDING SITE FOR RESIDUE 3SO D 502
3AC3SOFTWAREILE A:19 , PRO C:102 , ALA C:103 , SER C:104 , SER C:105 , PHE C:309 , PRO C:462 , GLU C:463BINDING SITE FOR RESIDUE 2SU C 501
4AC4SOFTWAREPRO B:102 , ALA B:103 , SER B:105 , PHE B:309 , PRO B:462 , GLU B:463 , ILE D:19BINDING SITE FOR RESIDUE 2SU B 501
5AC5SOFTWAREPHE B:98 , VAL B:99 , GLY B:159 , SER B:160 , HIS B:192 , SER B:194 , THR B:249 , ASP B:274 , ALA B:276 , ASP B:303 , LYS B:306 , HIS D:120 , TRP D:349 , THR D:356BINDING SITE FOR RESIDUE 3SO B 502
6AC6SOFTWAREHIS A:120 , TRP A:349 , THR A:356 , PHE C:98 , VAL C:99 , GLY C:159 , SER C:160 , HIS C:192 , SER C:194 , THR C:249 , ASP C:274 , ALA C:276 , ASP C:303 , LYS C:306BINDING SITE FOR RESIDUE 3SO A 501
7AC7SOFTWAREPRO A:102 , ALA A:103 , SER A:104 , SER A:105 , PHE A:309 , PRO A:462 , GLU A:463BINDING SITE FOR RESIDUE 2SU A 502
8AC8SOFTWAREPHE A:98 , VAL A:99 , GLY A:159 , SER A:160 , HIS A:192 , THR A:249 , ASP A:274 , ALA A:276 , ASP A:303 , HIS A:305 , LYS A:306 , HIS C:120 , LEU C:336 , LEU C:339 , TRP C:349 , THR C:356BINDING SITE FOR RESIDUE 3SO A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Tyr D:312 -Gly D:313
2Gly D:352 -Met D:353
3Tyr C:312 -Gly C:313
4Gly C:352 -Met C:353
5Tyr B:312 -Gly B:313
6Gly B:352 -Met B:353
7Tyr A:312 -Gly A:313
8Leu A:336 -Lys A:337
9Leu A:339 -Glu A:340
10Gly A:352 -Met A:353

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OBV)

(-) 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:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh........hhhhhhhhhhhhh....................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh...hhh.eeeeee...hhhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhhh.eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeeeehhhhh......eeeee..hhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhh.....eeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4obv A  16 TEYILNSTQLEEAIKSFVHDFCAEKHEIHDQPVVVEAKEHQEDKIKQIKIPEKGRPVNEVVSEMMNEVYRYRGDANHPRFFSFVPGPASSVSWLGDIMTSAYNIHAGGSKLAPMVNCIEQEVLKWLAKQVGFTENPGGVFVSGGSMANITALTAARDNKLTDINLHLGTAYISDQTHSSVAKGLRIIGITDSRIRRIPTNSHFQMDTTKLEEAIETDKKSGYIPFVVIGTAGTTNTGSIDPLTEISALCKKHDMWFHIDGAYGASVLLSPKYKSLLTGTGLADSISWDAHKWLFQTYGCAMVLVKDIRNLFHSFHVNPEYLKDLEDNVNTWDIGMELTRPARGLKLWLTLQVLGSDLIGSAIEHGFQLAVWAEEALNPKKDWEIVSPAQMAMINFRYAPKDLTKEEQDILNEKISHRILESGYAAIFTTVLNGKTVLRICAIHPEATQEDMQHTIDLLDQYGREIYTEMKK 489
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335    || 348       358       368       378       388       398       408       418       428       438       448       458       468       478       488 
                                                                                                                                                                                                                                                                                                                                                              340|                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                               344                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh........hhhhhhhhhhhhh....................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh...hhh.eeeeee...hhhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhhh.eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeeeehhhhh......eeeee..hhhhhhhhh.............hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhh.....eeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4obv B  16 TEYILNSTQLEEAIKSFVHDFCAEKHEIHDQPVVVEAKEHQEDKIKQIKIPEKGRPVNEVVSEMMNEVYRYRGDANHPRFFSFVPGPASSVSWLGDIMTSAYNIHAGGSKLAPMVNCIEQEVLKWLAKQVGFTENPGGVFVSGGSMANITALTAARDNKLTDINLHLGTAYISDQTHSSVAKGLRIIGITDSRIRRIPTNSHFQMDTTKLEEAIETDKKSGYIPFVVIGTAGTTNTGSIDPLTEISALCKKHDMWFHIDGAYGASVLLSPKYKSLLTGTGLADSISWDAHKWLFQTYGCAMVLVKDIRNLFHSFHVNPEYLKDLEDNVNTWDIGMELTRPARGLKLWLTLQVLGSDLIGSAIEHGFQLAVWAEEALNPKKDWEIVSPAQMAMINFRYAPKDLTKEEQDILNEKISHRILESGYAAIFTTVLNGKTVLRICAIHPEATQEDMQHTIDLLDQYGREIYTEMK 488
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335    || 348       358       368       378       388       398       408       418       428       438       448       458       468       478       488
                                                                                                                                                                                                                                                                                                                                                              340|                                                                                                                                                
                                                                                                                                                                                                                                                                                                                                                               344                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh........hhhhhhhhhhhhh....................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh...hhh.eeeeee...hhhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhhh.eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeeeehhhhh......eeeee..hhhhhhhhh.............hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhh.....eeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4obv C  16 TEYILNSTQLEEAIKSFVHDFCAEKHEIHDQPVVVEAKEHQEDKIKQIKIPEKGRPVNEVVSEMMNEVYRYRGDANHPRFFSFVPGPASSVSWLGDIMTSAYNIHAGGSKLAPMVNCIEQEVLKWLAKQVGFTENPGGVFVSGGSMANITALTAARDNKLTDINLHLGTAYISDQTHSSVAKGLRIIGITDSRIRRIPTNSHFQMDTTKLEEAIETDKKSGYIPFVVIGTAGTTNTGSIDPLTEISALCKKHDMWFHIDGAYGASVLLSPKYKSLLTGTGLADSISWDAHKWLFQTYGCAMVLVKDIRNLFHSFHVNPEYLKDLEDNVNTWDIGMELTRPARGLKLWLTLQVLGSDLIGSAIEHGFQLAVWAEEALNPKKDWEIVSPAQMAMINFRYAPKDLTKEEQDILNEKISHRILESGYAAIFTTVLNGKTVLRICAIHPEATQEDMQHTIDLLDQYGREIYTEMKK 489
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335    || 348       358       368       378       388       398       408       418       428       438       448       458       468       478       488 
                                                                                                                                                                                                                                                                                                                                                              340|                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                               344                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh........hhhhhhhhhhhhh....................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh...hhh.eeeeee...hhhhhhhhhhh..hhh.eeee........hhhhhhhhhhhhhhhh.eeeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhhhh..hhhhhhhhhhh.eeeeehhhhh......eeeee..hhhhhhhhh.............hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhh.....eeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4obv D  16 TEYILNSTQLEEAIKSFVHDFCAEKHEIHDQPVVVEAKEHQEDKIKQIKIPEKGRPVNEVVSEMMNEVYRYRGDANHPRFFSFVPGPASSVSWLGDIMTSAYNIHAGGSKLAPMVNCIEQEVLKWLAKQVGFTENPGGVFVSGGSMANITALTAARDNKLTDINLHLGTAYISDQTHSSVAKGLRIIGITDSRIRRIPTNSHFQMDTTKLEEAIETDKKSGYIPFVVIGTAGTTNTGSIDPLTEISALCKKHDMWFHIDGAYGASVLLSPKYKSLLTGTGLADSISWDAHKWLFQTYGCAMVLVKDIRNLFHSFHVNPEYLKDLEDNVNTWDIGMELTRPARGLKLWLTLQVLGSDLIGSAIEHGFQLAVWAEEALNPKKDWEIVSPAQMAMINFRYAPKDLTKEEQDILNEKISHRILESGYAAIFTTVLNGKTVLRICAIHPEATQEDMQHTIDLLDQYGREIYTEM 487
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335    || 348       358       368       378       388       398       408       418       428       438       448       458       468       478         
                                                                                                                                                                                                                                                                                                                                                              340|                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                                               344
   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 4OBV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        A7B1V0_RUMGN | A7B1V0: 4obu

(-) Related Entries Specified in the PDB File

4obu