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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHAN SYNTHASE FROM SALMONELLA TYPHIMURIUM WITH 2-AMINOPHENOL QUINONOID IN THE BETA SITE AND THE F6 INHIBITOR IN THE ALPHA SITE
 
Authors :  E. Hilario, D. Niks, M. F. Dunn, L. J. Mueller, L. Fan
Date :  06 May 13  (Deposition) - 01 Jan 14  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Carbon-Oxygen Lyase, Tryptophan Biosynthesis, F6F, Allosteric Enzyme, 2-Aminophenol Quinonoid, Biosynthesis, Aromatic Amino Acid Biosynthesis, Pyridoxal Phosphate, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Niks, E. Hilario, A. Dierkers, H. Ngo, D. Borchardt, T. J. Neubauer, L. Fan, L. J. Mueller, M. F. Dunn
Allostery And Substrate Channeling In The Tryptophan Synthase Bienzyme Complex: Evidence For Two Subunit Conformations And Four Quaternary States.
Biochemistry V. 52 6396 2013
PubMed-ID: 23952479  |  Reference-DOI: 10.1021/BI400795E

(-) Compounds

Molecule 1 - TRYPTOPHAN SYNTHASE ALPHA CHAIN
    Chains: A
    EC Number: 4.2.1.20
    Engineered: YES
    Expression System Cell Line: CB149
    Expression System Strain: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: DERIVATIVE OF PBR322
    Gene: TRPA
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
 
Molecule 2 - TRYPTOPHAN SYNTHASE BETA CHAIN
    Chains: B
    EC Number: 4.2.1.20
    Engineered: YES
    Expression System Cell Line: CB149
    Expression System Strain: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: DERIVATIVE OF PBR322
    Gene: TRPB
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 19)

Asymmetric/Biological Unit (6, 19)
No.NameCountTypeFull Name
1AQ31Ligand/IonN-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-3-[(2-HYDROXYPHENYL)AMINO]-D-ALANINE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3F6F1Ligand/Ion2-{[4-(TRIFLUOROMETHOXY)BENZOYL]AMINO}ETHYL DIHYDROGENPHOSPHATE
4NA3Ligand/IonSODIUM ION
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
6PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:49 , ALA A:59 , ILE A:64 , LEU A:100 , ALA A:129 , ILE A:153 , TYR A:175 , THR A:183 , GLY A:184 , PHE A:212 , GLY A:213 , GLY A:234 , SER A:235 , HOH A:422 , HOH A:438 , HOH A:444 , PRO B:18 , HOH B:527 , HOH B:563BINDING SITE FOR RESIDUE F6F A 301
02AC2SOFTWAREASN A:104 , ASN A:108 , HOH A:691 , ARG B:275 , VAL B:276 , GLN B:288BINDING SITE FOR RESIDUE NA A 302
03AC3SOFTWARESER A:168 , HOH A:756BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREARG A:179 , GLY A:181 , VAL A:182 , THR A:183 , GLY A:184 , ASN A:187 , HOH A:437 , HOH A:508 , HOH A:512 , HOH A:761BINDING SITE FOR RESIDUE PEG A 304
05AC5SOFTWAREARG A:15 , GLU A:16 , VAL A:224 , HOH A:773 , GLU B:40BINDING SITE FOR RESIDUE PEG A 305
06AC6SOFTWAREHIS B:86 , LYS B:87 , GLU B:109 , THR B:110 , GLY B:111 , ALA B:112 , GLY B:113 , GLN B:114 , HIS B:115 , LEU B:166 , THR B:190 , CYS B:230 , GLY B:232 , GLY B:233 , GLY B:234 , SER B:235 , ASN B:236 , GLY B:303 , GLU B:350 , SER B:377 , GLY B:378 , NA B:403BINDING SITE FOR RESIDUE AQ3 B 401
07AC7SOFTWAREGLY B:232 , PHE B:306 , SER B:308 , HOH B:505 , HOH B:857BINDING SITE FOR RESIDUE NA B 402
08AC8SOFTWARECYS B:230 , VAL B:231 , GLY B:234 , SER B:235 , ASN B:236 , ALA B:237 , AQ3 B:401BINDING SITE FOR RESIDUE NA B 403
09AC9SOFTWARELYS B:50 , GLN B:215 , LYS B:219 , PGE B:413 , HOH B:881 , HOH B:925 , HOH B:1029BINDING SITE FOR RESIDUE EDO B 404
10BC1SOFTWAREASN B:6 , GLY B:10 , HOH B:623 , HOH B:627 , HOH B:791BINDING SITE FOR RESIDUE EDO B 405
11BC2SOFTWARETHR B:66 , THR B:69 , ARG B:70 , THR B:71 , HOH B:889BINDING SITE FOR RESIDUE EDO B 406
12BC3SOFTWAREHIS B:273 , VAL B:325 , SER B:326 , HOH B:608 , HOH B:765 , HOH B:811BINDING SITE FOR RESIDUE EDO B 407
13BC4SOFTWAREGLU A:134 , LEU A:162 , HOH A:468 , HOH A:635 , HOH A:687 , GLN B:19 , MET B:22 , PRO B:23 , ASN B:26BINDING SITE FOR RESIDUE EDO B 408
14BC5SOFTWARELYS B:272 , GLU B:364 , HOH B:725 , HOH B:861BINDING SITE FOR RESIDUE EDO B 409
15BC6SOFTWAREARG B:275 , VAL B:276 , HOH B:502 , HOH B:708 , HOH B:749 , HOH B:963 , HOH B:982BINDING SITE FOR RESIDUE EDO B 410
16BC7SOFTWARETHR B:3 , LEU B:5BINDING SITE FOR RESIDUE EDO B 411
17BC8SOFTWAREGLU B:266 , SER B:297 , TYR B:298 , HOH B:599 , HOH B:764 , HOH B:1021BINDING SITE FOR RESIDUE EDO B 412
18BC9SOFTWAREGLU B:210 , GLU B:211 , ALA B:214 , EDO B:404 , HOH B:738 , HOH B:745 , HOH B:819 , HOH B:936 , HOH B:957BINDING SITE FOR RESIDUE PGE B 413
19CC1SOFTWAREASP B:47 , ASN B:51 , TYR B:52 , LEU B:59 , THR B:60 , LYS B:61 , GLN B:63 , LEU B:125 , LYS B:219 , GLU B:343 , HOH B:557 , HOH B:673 , HOH B:776BINDING SITE FOR RESIDUE PGE B 414

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:27 -Pro A:28
2Arg B:55 -Pro B:56
3His B:195 -Pro B:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KKX)

(-) Sequences/Alignments

Asymmetric/Biological 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4kkxa_ A: Trp synthase alpha-subunit                                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..eee.ee....hhhhhhhhhhhh...eeee...............hhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kkx A   1 MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLSRSGVTGAENRGALPLHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKIIEKNLASPKQMLAELRSFVSAMKAASRA 268
                                    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        


Chain B from PDB  Type:PROTEIN  Length:395
                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4kkxb_ B: Tryptophan synthase, beta-subunit                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.........eeeeeee.hhh.....hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhh.hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee.eeeeee..............hhhhh....hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kkx B   2 TTLLNPYFGEFGGMYVPQILMPALNQLEEAFVSAQKDPEFQAQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKSEIIAETGAGQHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLKDACNEALRDWSGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILDKEGRLPDAVIACVGGGSNAIGMFADFINDTSVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTADGQIEESYSISAGLDFPSVGPQHAYLNSIGRADYVSITDDEALEAFKTLCRHEGIIPALESSHALAHALKMMREQPEKEQLLVVNLSGRGDKDIFTVHDILKARGE 396
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  4kkx
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  TRPA_SALTY | P00929
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  TRPB_SALTY | P0A2K1
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  4.2.1.20
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRPA_SALTY | P00929: 1a50 1a5a 1a5b 1a5s 1beu 1bks 1c29 1c8v 1c9d 1cw2 1cx9 1fuy 1k3u 1k7e 1k7f 1k7x 1k8x 1k8y 1k8z 1kfb 1kfc 1kfe 1kfj 1kfk 1qop 1qoq 1tjp 1ttp 1ttq 1ubs 1wbj 2cle 2clf 2clh 2cli 2clk 2cll 2clm 2clo 2j9x 2j9y 2j9z 2rh9 2rhg 2trs 2tsy 2tys 2wsy 3cep 3pr2 4hn4 4hpj 4hpx 4ht3 4wx2 4xug 4y6g 4zqc 5bw6 5cgq
        TRPB_SALTY | P0A2K1: 1a50 1a5a 1a5b 1a5s 1beu 1bks 1c29 1c8v 1c9d 1cw2 1cx9 1fuy 1k3u 1k7e 1k7f 1k7x 1k8x 1k8y 1k8z 1kfb 1kfc 1kfe 1kfj 1kfk 1qop 1qoq 1tjp 1ttp 1ttq 1ubs 1wbj 2cle 2clf 2clh 2cli 2clk 2cll 2clm 2clo 2j9x 2j9y 2j9z 2rh9 2rhg 2trs 2tsy 2tys 2wsy 3cep 3pr2 4hn4 4hpj 4hpx 4ht3 4wx2 4xug 4y6g 4zqc 5bw6 5cgq

(-) Related Entries Specified in the PDB File

2cle TRYPTOPHAN SYNTHASE IN COMPLEX WITH N-(4'- TRIFLUOROMETHOXYBENZOYL)-2-AMINO-1-ETHYLPHOSPHATE (F6) - LOWF6 COMPLEX
2clf TRYPTOPHAN SYNTHASE IN COMPLEX WITH N-(4'- TRIFLUOROMETHOXYBENZOYL)-2-AMINO-1-ETHYLPHOSPHATE (F6) - HIGHF6 COMPLEX
2clm TRYPTOPHAN SYNTHASE (EXTERNAL ALDIMINE STATE) IN COMPLEX WITH N-(4'-TRIFLUOROMETHOXYBENZOYL)-2-AMINO-1- ETHYLPHOSPHATE (F6F)
3cep STRUCTURE OF A TRYPTOPHAN SYNTHASE QUINONOID INTERMEDIATE
3pr2 TRYPTOPHAN SYNTHASE INDOLINE QUINONOID STRUCTURE WITH F9 INHIBITOR IN ALPHA SITE
4hpj CRYSTAL STRUCTURE OF TRYPTOPHAN SYNTHASE AT 1.45 RESOLUTION IN COMPLEX WITH 2-AMINOPHENOL QUINONOID IN THE BETA SITE AND THE F9 INHIBITOR IN THE ALPHA SITE.