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(-) Description

Title :  CRYSTAL STRUCTURE OF INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE (TRPC) FROM THERMUS THERMOPHILUS AT 1.8 A RESOLUTION
 
Authors :  B. Bagautdinov, T. H. Tahirov, Riken Structural Genomics/Proteomi Initiative (Rsgi)
Date :  04 Mar 04  (Deposition) - 23 Mar 04  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Biol. Unit 4:  A (1x),B (1x)
Keywords :  Lyase, Tryptophan Biosynthesis, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, K. Yutani
Structure Of Indole-3-Glycerol Phosphate Synthase From Thermus Thermophilus Hb8: Implications For Thermal Stability.
Acta Crystallogr. , Sect. D V. 67 1054 2011
PubMed-ID: 22120743  |  Reference-DOI: 10.1107/S0907444911045264

(-) Compounds

Molecule 1 - INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 4.1.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TRPC
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1ACY5Ligand/IonACETIC ACID
2GOL1Ligand/IonGLYCEROL
3SO410Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2GOL-1Ligand/IonGLYCEROL
3SO45Ligand/IonSULFATE ION
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2GOL1Ligand/IonGLYCEROL
3SO45Ligand/IonSULFATE ION
Biological Unit 3 (3, 9)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2GOL1Ligand/IonGLYCEROL
3SO45Ligand/IonSULFATE ION
Biological Unit 4 (2, 7)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2GOL-1Ligand/IonGLYCEROL
3SO45Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:53 , SER A:215 , GLY A:216 , ILE A:235 , GLY A:236 , THR A:237 , HOH A:3007 , HOH A:3064 , HOH A:3149BINDING SITE FOR RESIDUE SO4 A 2001
02AC2SOFTWAREARG A:43 , ARG A:80 , HOH A:3031 , HOH A:3181 , ARG B:43 , ARG B:80 , HOH B:3012BINDING SITE FOR RESIDUE SO4 A 2002
03AC3SOFTWARELYS B:53 , SER B:215 , GLY B:216 , ILE B:235 , GLY B:236 , THR B:237 , HOH B:3006 , HOH B:3039 , HOH B:3048 , HOH B:3245 , HOH B:3346BINDING SITE FOR RESIDUE SO4 B 2003
04AC4SOFTWARELYS A:53 , SER A:56 , PRO A:57 , SER A:58 , PHE A:91 , THR A:237 , HOH A:3050 , HOH A:3126BINDING SITE FOR RESIDUE SO4 A 2004
05AC5SOFTWARETHR B:163 , GLU B:164 , ARG B:197 , HOH B:3071 , HOH B:3192 , HOH B:3230BINDING SITE FOR RESIDUE SO4 B 2005
06AC6SOFTWAREMET B:1 , ARG B:2 , ARG B:76 , HOH B:3047 , HOH B:3198BINDING SITE FOR RESIDUE SO4 B 2006
07AC7SOFTWARETHR A:163 , ARG A:165 , HOH A:3302 , HOH B:3337BINDING SITE FOR RESIDUE SO4 A 2007
08AC8SOFTWARETHR A:163 , GLU A:164 , ARG A:197 , HOH A:3212 , HOH A:3302 , LYS B:220 , GLU B:251BINDING SITE FOR RESIDUE SO4 B 2008
09AC9SOFTWAREPRO A:44 , GLY A:45 , HOH A:3326 , ARG B:250BINDING SITE FOR RESIDUE SO4 A 2009
10BC1SOFTWAREARG A:250 , PRO B:44 , GLY B:45BINDING SITE FOR RESIDUE SO4 B 2010
11BC2SOFTWAREMET A:1 , ARG A:2 , HOH A:3114 , HOH A:3275 , HOH A:3292BINDING SITE FOR RESIDUE ACY A 3001
12BC3SOFTWARELYS B:53 , SER B:58 , ARG B:183 , HOH B:3049 , HOH B:3051 , HOH B:3058 , HOH B:3346BINDING SITE FOR RESIDUE ACY B 3002
13BC4SOFTWAREARG B:63 , PRO B:243 , ASP B:244 , LEU B:245 , HOH B:3024BINDING SITE FOR RESIDUE ACY B 3003
14BC5SOFTWARESER A:33 , VAL A:34 , ARG A:125 , HOH A:3063 , HOH A:3077BINDING SITE FOR RESIDUE ACY A 3004
15BC6SOFTWAREARG B:19 , ARG B:111 , MET B:120 , GLU B:123 , HOH B:3138BINDING SITE FOR RESIDUE ACY B 3005
16BC7SOFTWARELEU B:201 , ARG B:205 , HOH B:3325BINDING SITE FOR RESIDUE GOL B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VC4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VC4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VC4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VC4)

(-) Exons   (0, 0)

(no "Exon" information available for 1VC4)

(-) 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:254
 aligned with P84126_THETH | P84126 from UniProtKB/TrEMBL  Length:254

    Alignment length:254
                                    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    
         P84126_THETH     1 MRPDLSRVPGVLGEIARKRASEVAPYPLPEPPSVPSFKEALLRPGLSVIAEVKRQSPSEGLIREVDPVEAALAYARGGARAVSVLTEPHRFGGSLLDLKRVREAVDLPLLRKDFVVDPFMLEEARAFGASAALLIVALLGELTGAYLEEARRLGLEALVEVHTERELEIALEAGAEVLGINNRDLATLHINLETAPRLGRLARKRGFGGVLVAESGYSRKEELKALEGLFDAVLIGTSLMRAPDLEAALRELVG 254
               SCOP domains d1vc4a_ A: Indole-3-glycerophosphate synthase, IPGS                                                                                                                                                                                                            SCOP domains
               CATH domains 1vc4A00 A:1-254 Aldolase class I                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.............hhhhhhh....eeeeee.............hhhhhhhhhhhh...eeeee........hhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeeehhhhh.hhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh....eeeee....hhhhhhh......eeeehhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vc4 A   1 MRPDLSRVPGVLGEIARKRASEVAPYPLPEPPSVPSFKEALLRPGLSVIAEVKRQSPSEGLIREVDPVEAALAYARGGARAVSVLTEPHRFGGSLLDLKRVREAVDLPLLRKDFVVDPFMLEEARAFGASAALLIVALLGELTGAYLEEARRLGLEALVEVHTERELEIALEAGAEVLGINNRDLATLHINLETAPRLGRLARKRGFGGVLVAESGYSRKEELKALEGLFDAVLIGTSLMRAPDLEAALRELVG 254
                                    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    


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with P84126_THETH | P84126 from UniProtKB/TrEMBL  Length:254

    Alignment length:254
                                    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    
         P84126_THETH     1 MRPDLSRVPGVLGEIARKRASEVAPYPLPEPPSVPSFKEALLRPGLSVIAEVKRQSPSEGLIREVDPVEAALAYARGGARAVSVLTEPHRFGGSLLDLKRVREAVDLPLLRKDFVVDPFMLEEARAFGASAALLIVALLGELTGAYLEEARRLGLEALVEVHTERELEIALEAGAEVLGINNRDLATLHINLETAPRLGRLARKRGFGGVLVAESGYSRKEELKALEGLFDAVLIGTSLMRAPDLEAALRELVG 254
               SCOP domains d1vc4b_ B: Indole-3-glycerophosphate synthase, IPGS                                                                                                                                                                                                            SCOP domains
               CATH domains 1vc4B00 B:1-254 Aldolase class I                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) -------------IGPS-1vc4B01 B:14-252                                                                                                                                                                                                                          -- Pfam domains (1)
           Pfam domains (2) -------------IGPS-1vc4B02 B:14-252                                                                                                                                                                                                                          -- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhhhh............hhhhhhh....eeeeee..ee...ee....hhhhhhhhhhhh...eeeee........hhhhhhhhhhhh...eeee.....hhhhhhhhhh...eeeeehhhhh.hhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeeee...........hhhhhhhhhhhhh....eeeee....hhhhhhh......eeeehhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vc4 B   1 MRPDLSRVPGVLGEIARKRASEVAPYPLPEPPSVPSFKEALLRPGLSVIAEVKRQSPSEGLIREVDPVEAALAYARGGARAVSVLTEPHRFGGSLLDLKRVREAVDLPLLRKDFVVDPFMLEEARAFGASAALLIVALLGELTGAYLEEARRLGLEALVEVHTERELEIALEAGAEVLGINNRDLATLHINLETAPRLGRLARKRGFGGVLVAESGYSRKEELKALEGLFDAVLIGTSLMRAPDLEAALRELVG 254
                                    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
   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  (1, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)
(-)
Family: IGPS (10)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (P84126_THETH | P84126)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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:0004425    indole-3-glycerol-phosphate synthase activity    Catalysis of the reaction: 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate = 1-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O.
    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.
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.

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  1vc4
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  P84126_THETH | P84126
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