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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT FROM ESCHERICHIA COLI
 
Authors :  K. Nishio, Y. Morimoto, M. Ishizuka, K. Ogasahara, K. Yutani, T. Tsukih Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 Sep 04  (Deposition) - 15 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Tryptophan Synthase, Tryptophan, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Nishio, Y. Morimoto, M. Ishizuka, K. Ogasahara, T. Tsukihara, K. Yutani
Conformational Changes In The Alpha-Subunit Coupled To Binding Of The Beta(2)-Subunit Of Tryptophan Synthase From Escherichia Coli: Crystal Structure Of The Tryptophan Synthase Alpha-Subunit Alon
Biochemistry V. 44 1184 2005
PubMed-ID: 15667212  |  Reference-DOI: 10.1021/BI047927M

(-) Compounds

Molecule 1 - TRYPTOPHAN SYNTHASE ALPHA CHAIN
    Chains: A, B
    EC Number: 4.2.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC8PTRPA(WILD)-TRPA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2SO413Ligand/IonSULFATE ION
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 3 (2, 42)
No.NameCountTypeFull Name
1GOL16Ligand/IonGLYCEROL
2SO426Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:69 , ARG A:70 , ALA A:71 , PHE B:1212 , GLY B:1213 , SER B:1233 , GLY B:1234 , SER B:1235 , HOH B:2003BINDING SITE FOR RESIDUE SO4 B 501
02AC2SOFTWAREPHE A:212 , GLY A:213 , SER A:233 , GLY A:234 , SER A:235 , HOH A:2002 , HOH A:2070 , LEU B:1069 , ARG B:1070 , ALA B:1071BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREARG B:1179 , LEU B:1193 , GLN B:1210 , HOH B:2024 , HOH B:2074 , HOH B:2089BINDING SITE FOR RESIDUE SO4 B 503
04AC4SOFTWAREARG A:179 , LEU A:193 , GLN A:210 , HOH A:2104BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWAREARG A:171 , GLY B:1110 , ILE B:1111 , ASP B:1112 , HOH B:2054BINDING SITE FOR RESIDUE SO4 B 505
06AC6SOFTWAREGOL B:606 , LYS B:1120 , ASP B:1159 , ASP B:1160 , ARG B:1188BINDING SITE FOR RESIDUE SO4 B 506
07AC7SOFTWAREILE B:1030 , GLU B:1031 , HOH B:2009BINDING SITE FOR RESIDUE SO4 B 507
08AC8SOFTWAREGLU A:247 , PRO A:248 , GLU A:249 , LYS A:250BINDING SITE FOR RESIDUE SO4 A 508
09AC9SOFTWARELYS A:35 , GLU B:1247 , PRO B:1248 , GLU B:1249 , LYS B:1250BINDING SITE FOR RESIDUE SO4 B 509
10BC1SOFTWAREASN A:157 , ALA A:158 , ASP A:159 , LEU A:162 , ARG A:188 , HOH A:2139BINDING SITE FOR RESIDUE SO4 A 510
11BC2SOFTWAREARG A:70 , SER B:1215BINDING SITE FOR RESIDUE SO4 A 511
12BC3SOFTWAREGLY A:29 , ILE A:30 , GLU A:31 , HOH A:2046BINDING SITE FOR RESIDUE SO4 A 512
13BC4SOFTWARELYS A:120 , ASP A:160BINDING SITE FOR RESIDUE SO4 A 513
14BC5SOFTWARELYS A:120 , HIS A:195 , LYS A:199BINDING SITE FOR RESIDUE GOL A 601
15BC6SOFTWAREARG A:140 , LEU A:144 , PRO A:150 , SER A:168 , TYR A:169 , ARG A:171 , PHE B:1107 , ASN B:1108 , LYS B:1109 , HOH B:2099BINDING SITE FOR RESIDUE GOL A 602
16BC7SOFTWARETYR A:115 , VAL A:126 , LEU A:127 , VAL A:128 , VAL A:131 , SER A:136 , PHE A:139 , PRO A:150 , ILE A:151 , PHE A:152BINDING SITE FOR RESIDUE GOL A 603
17BC8SOFTWARETYR B:1115 , VAL B:1126 , LEU B:1127 , VAL B:1128 , SER B:1136 , PHE B:1139 , PRO B:1150 , ILE B:1151 , PHE B:1152BINDING SITE FOR RESIDUE GOL B 604
18BC9SOFTWAREALA A:86 , ARG A:89 , GLN A:90 , LYS A:120 , VAL A:121 , HIS A:195BINDING SITE FOR RESIDUE GOL A 605
19CC1SOFTWARESO4 B:506 , LYS B:1120 , ASP B:1160 , LYS B:1199BINDING SITE FOR RESIDUE GOL B 606
20CC2SOFTWAREGLU A:2 , ARG A:171 , GLY A:172 , ALA A:206 , HOH A:2120BINDING SITE FOR RESIDUE GOL A 607
21CC3SOFTWARESER A:55 , PHE A:72 , HOH A:2110 , THR B:1024 , GLY B:1051 , ILE B:1052BINDING SITE FOR RESIDUE GOL A 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WQ5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:27 -Pro A:28
2Asp B:1027 -Pro B:1028

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WQ5)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_ECOLI48-61
 		  2A:48-56
B:1048-1058
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_ECOLI48-61
 		  1A:48-56
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_ECOLI48-61
 		  1-
B:1048-1058
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_ECOLI48-61
 		  4A:48-56
B:1048-1058

(-) Exons   (0, 0)

(no "Exon" information available for 1WQ5)

(-) 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:258
 aligned with TRPA_ECOLI | P0A877 from UniProtKB/Swiss-Prot  Length:268

    Alignment length: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        
          TRPA_ECOLI      1 MERYESLFAQLKERKEGAFVPFVTLGDPGIEQSLKIIDTLIEAGADALELGIPFSDPLADGPTIQNATLRAFAAGVTPAQCFEMLALIRQKHPTIPIGLLMYANLVFNKGIDEFYAQCEKVGVDSVLVADVPVEESAPFRQAALRHNVAPIFICPPNADDDLLRQIASYGRGYTYLLSRAGVTGAENRAALPLNHLVAKLKEYNAAPPLQGFGISAPDQVKAAIDAGAAGAISGSAIVKIIEQHINEPEKMLAALKVFVQPMKAATRS  268
               SCOP domains d1wq5a_ A: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1wq5A00 A:1-268 Aldolase class I                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh....eeee.....--------....hhhhhh..hhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh..ee..ee....hhhhhhhhhhhh...eeee.hhhh.--......hhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------TRP_SYNTHASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wq5 A    1 MERYESLFAQLKERKEGAFVPFVTLGDPGIEQSLKIIDTLIEAGADALELGIPFSD--------QNATLRAFAAGVTPAQCFEMLALIRQKHPTIPIGLLMYANLVFNKGIDEFYAQCEKVGVDSVLVADVPVEESAPFRQAALRHNVAPIFICPPNADDDLLRQIASYGRGYTYLLSRAGVT--ENRAALPLNHLVAKLKEYNAAPPLQGFGISAPDQVKAAIDAGAAGAISGSAIVKIIEQHINEPEKMLAALKVFVQPMKAATRS  268
                                    10        20        30        40        50     |   -    |   70        80        90       100       110       120       130       140       150       160       170       180  |  | 190       200       210       220       230       240       250       260        
                                                                                  56       65                                                                                                                   183  |                                                                                  
                                                                                                                                                                                                                   186                                                                                  


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with TRPA_ECOLI | P0A877 from UniProtKB/Swiss-Prot  Length:268

    Alignment length: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        
          TRPA_ECOLI      1 MERYESLFAQLKERKEGAFVPFVTLGDPGIEQSLKIIDTLIEAGADALELGIPFSDPLADGPTIQNATLRAFAAGVTPAQCFEMLALIRQKHPTIPIGLLMYANLVFNKGIDEFYAQCEKVGVDSVLVADVPVEESAPFRQAALRHNVAPIFICPPNADDDLLRQIASYGRGYTYLLSRAGVTGAENRAALPLNHLVAKLKEYNAAPPLQGFGISAPDQVKAAIDAGAAGAISGSAIVKIIEQHINEPEKMLAALKVFVQPMKAATRS  268
               SCOP domains d1wq5b_ B: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1wq5B00 B:1001-1268 Aldolase class I                                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhh...eeee.......-----.....hhhhh...hhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..ee..ee....hhhhhhhhhhhh...eeee.hhhh.--......hhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------TRP_SYNTHASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wq5 B 1001 MERYESLFAQLKERKEGAFVPFVTLGDPGIEQSLKIIDTLIEAGADALELGIPFSDPL-----IQNATLRAFAAGVTPAQCFEMLALIRQKHPTIPIGLLMYANLVFNKGIDEFYAQCEKVGVDSVLVADVPVEESAPFRQAALRHNVAPIFICPPNADDDLLRQIASYGRGYTYLLSRAGVT--ENRAALPLNHLVAKLKEYNAAPPLQGFGISAPDQVKAAIDAGAAGAISGSAIVKIIEQHINEPEKMLAALKVFVQPMKAATRS 1268
                                  1010      1020      1030      1040      1050       | -   |  1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180  |  |1190      1200      1210      1220      1230      1240      1250      1260        
                                                                                  1058  1064                                                                                                                   1183  |                                                                                  
                                                                                                                                                                                                                  1186
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WQ5)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRPA_ECOLI | P0A877)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0004834    tryptophan synthase activity    Catalysis of the reaction: L-serine + (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000162    tryptophan biosynthetic process    The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRPA_ECOLI | P0A877: 1v7y 1xc4 1xcf

(-) Related Entries Specified in the PDB File

1v7y ROOM-TEMPERATURE CRYSTAL STRUCTURE RELATED ID: MY_001000019.1 RELATED DB: TARGETDB