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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM TRYPTOPHAN SYNTHASE AT 1.30A COMPLEXED WITH N-(4'-TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE (F9) INHIBITOR IN THE ALPHA SITE, INTERNAL ALDIMINE
 
Authors :  E. Hilario, D. Niks, M. F. Dunn, L. J. Mueller, L. Fan
Date :  31 Oct 12  (Deposition) - 01 Jan 14  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (2x),B (2x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  A (1x),B (1x)
Keywords :  Lyase, Carbon-Oxygen Lyase, Tryptophan Biosynthesis, Salmonella, F9F, Allosteric Enzyme, Amino-Acid Biosynthesis, Aromatic Amino Acid Biosynthesis, Pyridoxal Phosphate, Cesium Ion, 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: ESCHERICHIA COLI
    Expression System Strain: CB149
    Expression System Taxid: 562
    Expression System Vector Type: DERIVATIVE OF PBR322
    Gene: STM1727, 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: ESCHERICHIA COLI
    Expression System Strain: CB149
    Expression System Taxid: 562
    Expression System Vector Type: DERIVATIVE OF PBR322
    Gene: STM1726, TRPB
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): A (2x)B (2x)
Biological Unit 3 (2x): AB
Biological Unit 4 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 32)

Asymmetric Unit (9, 32)
No.NameCountTypeFull Name
1BCN4Ligand/IonBICINE
2CL7Ligand/IonCHLORIDE ION
3CS3Ligand/IonCESIUM ION
4EDO10Ligand/Ion1,2-ETHANEDIOL
5F9F1Ligand/Ion2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYLDIHYDROGEN PHOSPHATE
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
7PG51Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
8PGE3Ligand/IonTRIETHYLENE GLYCOL
9PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (7, 22)
No.NameCountTypeFull Name
1BCN4Ligand/IonBICINE
2CL-1Ligand/IonCHLORIDE ION
3CS-1Ligand/IonCESIUM ION
4EDO10Ligand/Ion1,2-ETHANEDIOL
5F9F1Ligand/Ion2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYLDIHYDROGEN PHOSPHATE
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
7PG51Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
8PGE3Ligand/IonTRIETHYLENE GLYCOL
9PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (5, 30)
No.NameCountTypeFull Name
1BCN6Ligand/IonBICINE
2CL-1Ligand/IonCHLORIDE ION
3CS-1Ligand/IonCESIUM ION
4EDO14Ligand/Ion1,2-ETHANEDIOL
5F9F-1Ligand/Ion2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYLDIHYDROGEN PHOSPHATE
6PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
7PG5-1Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
8PGE4Ligand/IonTRIETHYLENE GLYCOL
9PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 3 (7, 44)
No.NameCountTypeFull Name
1BCN8Ligand/IonBICINE
2CL-1Ligand/IonCHLORIDE ION
3CS-1Ligand/IonCESIUM ION
4EDO20Ligand/Ion1,2-ETHANEDIOL
5F9F2Ligand/Ion2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYLDIHYDROGEN PHOSPHATE
6PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
7PG52Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
8PGE6Ligand/IonTRIETHYLENE GLYCOL
9PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 4 (5, 15)
No.NameCountTypeFull Name
1BCN3Ligand/IonBICINE
2CL-1Ligand/IonCHLORIDE ION
3CS-1Ligand/IonCESIUM ION
4EDO7Ligand/Ion1,2-ETHANEDIOL
5F9F-1Ligand/Ion2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYLDIHYDROGEN PHOSPHATE
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
7PG5-1Ligand/Ion1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
8PGE2Ligand/IonTRIETHYLENE GLYCOL
9PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:22 , GLU A:49 , ALA A:59 , ILE A:64 , LEU A:100 , LEU A:127 , ALA A:129 , ILE A:153 , TYR A:175 , THR A:183 , GLY A:184 , PHE A:212 , GLY A:213 , ILE A:232 , GLY A:234 , SER A:235 , HOH A:406 , HOH A:411 , HOH A:415 , PRO B:18BINDING SITE FOR RESIDUE F9F A 301
02AC2SOFTWARESER A:247 , PRO A:248 , LYS A:249 , GLN A:250BINDING SITE FOR RESIDUE BCN A 302
03AC3SOFTWARESER A:221 , ALA A:265 , ARG A:267 , LYS B:99BINDING SITE FOR RESIDUE CS A 304
04AC4SOFTWAREPHE A:107 , ILE A:111 , GLU A:135 , PRO A:138 , PHE A:139 , HOH A:416 , HOH A:435 , HOH A:601 , HOH A:674 , TYR B:16 , LYS B:283BINDING SITE FOR RESIDUE PGE A 305
05AC5SOFTWAREARG A:164 , VAL A:166 , ALA A:167 , SER A:168 , GLY A:170 , ARG A:171 , THR A:174 , TYR A:203 , HIS A:204 , ALA A:205 , ALA A:206 , HOH A:663BINDING SITE FOR RESIDUE PG5 A 306
06AC6SOFTWAREPRO A:93 , ALA A:137 , ARG A:140 , GLN A:141 , EDO A:308 , HOH A:455BINDING SITE FOR RESIDUE EDO A 307
07AC7SOFTWAREPRO A:93 , THR A:94 , EDO A:307 , HOH A:430BINDING SITE FOR RESIDUE EDO A 308
08AC8SOFTWAREALA A:86 , LEU A:87 , GLU A:90 , ARG A:171 , HOH A:482 , HOH A:487BINDING SITE FOR RESIDUE EDO A 309
09AC9SOFTWAREHIS B:86 , LYS B:87 , GLN B:114 , 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 , HOH B:502 , HOH B:684 , HOH B:937BINDING SITE FOR RESIDUE PLP B 401
10BC1SOFTWARELYS B:87 , THR B:110 , GLY B:111 , ALA B:112 , GLY B:113 , GLN B:114 , HIS B:115 , EDO B:419BINDING SITE FOR RESIDUE EDO B 402
11BC2SOFTWARELEU B:271 , LYS B:272 , GLY B:274 , PRO B:285 , ASN B:317 , GLU B:364 , CL B:423 , HOH B:893BINDING SITE FOR RESIDUE PGE B 403
12BC3SOFTWAREALA B:67BINDING SITE FOR RESIDUE CL B 404
13BC4SOFTWAREGLY B:259 , HIS B:260 , GLU B:263 , THR B:328 , ASP B:329 , ASP B:330 , EDO B:413 , EDO B:414 , HOH B:539 , HOH B:771 , HOH B:773 , HOH B:897 , HOH B:904BINDING SITE FOR RESIDUE BCN B 405
14BC5SOFTWARETHR B:248 , VAL B:250 , GLY B:251 , LEU B:252 , GLY B:320 , ARG B:321 , ASP B:323 , HOH B:780 , HOH B:803 , HOH B:856BINDING SITE FOR RESIDUE BCN B 406
15BC6SOFTWARETHR B:289 , ALA B:290 , ASP B:291 , GLN B:293 , HOH B:581 , HOH B:599 , HOH B:764BINDING SITE FOR RESIDUE BCN B 407
16BC7SOFTWAREVAL B:117BINDING SITE FOR RESIDUE CL B 408
17BC8SOFTWAREASP B:47 , LYS B:61 , LYS B:219 , PEG B:416 , HOH B:522 , HOH B:553 , HOH B:795BINDING SITE FOR RESIDUE EDO B 409
18BC9SOFTWAREHIS B:273 , VAL B:325 , SER B:326 , HOH B:578 , HOH B:664 , HOH B:716 , HOH B:794BINDING SITE FOR RESIDUE EDO B 410
19CC1SOFTWARETHR B:66 , THR B:69 , THR B:71 , HOH B:822 , HOH B:948BINDING SITE FOR RESIDUE CS B 411
20CC2SOFTWAREVAL B:231 , GLY B:232 , GLU B:256 , GLY B:268 , PRO B:270 , LEU B:304 , PHE B:306 , SER B:308BINDING SITE FOR RESIDUE CS B 412
21CC3SOFTWAREASP B:330 , GLU B:331 , BCN B:405 , EDO B:414 , HOH B:586 , HOH B:693 , HOH B:771BINDING SITE FOR RESIDUE EDO B 413
22CC4SOFTWARETHR B:328 , BCN B:405 , EDO B:413BINDING SITE FOR RESIDUE EDO B 414
23CC5SOFTWARETHR B:3 , LEU B:4 , ASN B:6BINDING SITE FOR RESIDUE PEG B 415
24CC6SOFTWAREASN B:51 , TYR B:52 , THR B:60 , LYS B:61 , LEU B:125 , GLU B:343 , EDO B:409 , HOH B:870BINDING SITE FOR RESIDUE PEG B 416
25CC7SOFTWAREGLU B:211 , ALA B:214 , GLN B:215 , HOH B:524 , HOH B:544 , HOH B:605 , HOH B:751 , HOH B:756BINDING SITE FOR RESIDUE PGE B 417
26CC8SOFTWAREGLY B:10BINDING SITE FOR RESIDUE CL B 418
27CC9SOFTWAREGLU B:109 , GLY B:189 , PHE B:306 , EDO B:402BINDING SITE FOR RESIDUE EDO B 419
28DC1SOFTWAREASP B:225 , HOH B:528BINDING SITE FOR RESIDUE CL B 420
29DC2SOFTWAREHOH B:669 , HOH B:759 , HOH B:852BINDING SITE FOR RESIDUE EDO B 421
30DC3SOFTWAREASP B:225 , SER B:249 , HOH B:821BINDING SITE FOR RESIDUE CL B 422
31DC4SOFTWAREPHE B:12 , PRO B:285 , PGE B:403 , HOH B:516 , HOH B:739BINDING SITE FOR RESIDUE CL B 423

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HT3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:27 -Pro A:28
2Pro A:192 -Leu A:193
3Arg B:55 -Pro B:56
4His B:195 -Pro B:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HT3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HT3)

(-) Exons   (0, 0)

(no "Exon" information available for 4HT3)

(-) 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4ht3a_ 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..ee..ee....hhhhhhhhhhhh...eeee...............hhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ht3 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:393
                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4ht3b_ B: Tryptophan synthase, beta-subunit                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhh...eeeeeee.hhh....hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee.eeeeee..............hhhhh....hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ht3 B   2 TTLLNPYFGEFGGMYVPQILMPALNQLEEAFVSAQKDPEFQAQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKSEIIAETGAGQHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLKDACNEALRDWSGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILDKEGRLPDAVIACVGGGSNAIGMFADFINDTSVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTADGQIEESYSISAGLDFPSVGPQHAYLNSIGRADYVSITDDEALEAFKTLCRHEGIIPALESSHALAHALKMMREQPEKEQLLVVNLSGRGDKDIFTVHDILKAR 394
                                    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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HT3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HT3)

(-) Gene Ontology  (12, 21)

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Access by UniProt ID/Accession number
  TRPA_SALTY | P00929
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TRPB_SALTY | P0A2K1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4kkx 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 4kkx 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
2cli TRYPTOPHAN SYNTHASE IN COMPLEX WITH N-(4'- TRIFLUOROMETHOXYBENZENESULFONYL)-2-AMINO-1-ETHYLPHOSPHATE (F9)
2rh9 TRYPTOPHAN SYNTHASE COMPLEXED WITH IGP, INTERNAL ALDIMINE, PH 9.0
2rhg TRYPTOPHAN SYNTHASE COMPLEXED WITH IGP, PH 7.0, INTERNAL ALDIMINE
4hn4
4hpj
4hpx