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(-) Description

Title :  STEREOISOMER OF PRPP BOUND IN THE ACTIVE SITE OF MYCOBACTERIUM TUBERCULOSIS ANTHRANILATE PHOSPHORIBOSYL (ANPRT; TRPD)
 
Authors :  G. L. Evans, E. N. Baker, J. S. Lott, Tb Structural Genomics Consorti (Tbsgc)
Date :  15 Jun 15  (Deposition) - 20 Jul 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Stereoisomer Of Prpp, Phosphoriboysl Pyrophosphate, Tb Structural Genomics Consortium, Tbsgc, Magnesium Binding, Transferase, Psi-2, Protein Structure Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. L. Evans, E. N. Baker, J. S. Lott
Binding And Mimicking Of The Phosphate-Rich Substrate, Prpp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.2.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET23A
    Expression System Strain: BL21(DE3)PGROESL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TRPD, RV2192C, MTCY190.03C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
151N2Ligand/Ion5-O-[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]-1-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE
2GOL1Ligand/IonGLYCEROL
3MG4Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:119 , GLU A:252 , 51N A:403 , HOH A:524 , HOH A:594binding site for residue MG A 401
2AC2SOFTWAREASP A:111 , VAL A:113 , HOH A:505 , HOH A:511 , HOH A:601 , HOH A:639binding site for residue MG A 402
3AC3SOFTWAREVAL A:106 , GLY A:107 , GLY A:109 , GLY A:110 , ASN A:117 , LEU A:118 , SER A:119 , THR A:120 , LYS A:135 , ASN A:138 , ARG A:139 , ALA A:140 , ALA A:141 , SER A:142 , SER A:143 , GLU A:252 , MG A:401 , HOH A:511 , HOH A:524 , HOH A:527 , HOH A:535 , HOH A:556 , HOH A:557 , HOH A:589 , HOH A:606 , HOH A:674binding site for residue 51N A 403
4AC4SOFTWAREPHE A:274 , ASP A:275 , GLY A:278 , TRP A:336 , ARG B:194binding site for residue GOL A 404
5AC5SOFTWARESER B:119 , GLU B:252 , 51N B:403 , HOH B:534 , HOH B:600binding site for residue MG B 401
6AC6SOFTWAREASP B:111 , VAL B:113 , HOH B:515 , HOH B:559 , HOH B:636 , HOH B:709binding site for residue MG B 402
7AC7SOFTWAREVAL B:106 , GLY B:107 , GLY B:109 , GLY B:110 , ASN B:117 , LEU B:118 , SER B:119 , THR B:120 , LYS B:135 , ASN B:138 , ARG B:139 , ALA B:140 , ALA B:141 , SER B:142 , SER B:143 , GLU B:252 , MG B:401 , HOH B:504 , HOH B:514 , HOH B:534 , HOH B:536 , HOH B:559 , HOH B:579 , HOH B:585 , HOH B:598 , HOH B:612 , HOH B:672binding site for residue 51N B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C1R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C1R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C1R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C1R)

(-) Exons   (0, 0)

(no "Exon" information available for 5C1R)

(-) 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:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh............eeeee.........hhhhhhhhhhhhh...eeeee........hhhhhhhhh......hhhhhhhhhhhh.eeeeehhhhh..hhhhhhhhhhhh..hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeeee............eeeeeee..eeeeeeehhhhhh....hhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c1r A  25 PSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTGGDGVNTVNLSTMAAIVVAAAGVPVVKHGNRAASSLSGGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAGLSAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQ 369
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      |336       346       356       366   
                                                                                                                                                                                                                                                                                                                                            331|                                   
                                                                                                                                                                                                                                                                                                                                             334                                   


Chain B from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh............eeeee.........hhhhhhhhhhhhh...eeeee........hhhhhhhhh......hhhhhhhhhhhhheeeeehhhhh..hhhhhhhhhhhh..hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeeee............eeeeeee..eeeeeeehhhhhh....hhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c1r B  24 VPSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTGGDGVNTVNLSTMAAIVVAAAGVPVVKHGNRAASSLSGGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRREIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAGLSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQI 370
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       334       344       354       364      
                                                                                                                                                                                                                                                                                                                                             331|                                     
                                                                                                                                                                                                                                                                                                                                              333
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 5C1R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C1R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C1R)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  5c1r
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  TRPD_MYCTU | P9WFX5
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRPD_MYCTU | P9WFX5: 1zvw 2bpq 3qqs 3qr9 3qs8 3qsa 3r6c 3r88 3twp 3uu1 4giu 4gkm 4ij1 4m0r 4n5v 4n8q 4n93 4owm 4own 4owo 4owq 4ows 4owu 4owv 4x58 4x59 4x5a 4x5b 4x5c 4x5d 4x5e 5bne 5byt 5c2l 5c7s

(-) Related Entries Specified in the PDB File

1zvw 1ZVW CONTAINS THE SAME PROTEIN WITH RELATED LIGAND, PRPP, BUT CRYSTALLIZED IN DIFFERENT CONDITION WITH DIFFERENT UNIT CELL AND SPACE GROUP
3byt 3BYT CONTAINS THE SAME PROTEIN WITH RELATED LIGAND, PRPP, CRYSTALLIZED IN SAME CONDITION, BUT WITH DIFFERENT UNIT CELL AND SPACE GROUP
3qr9 3QR9 CONTAINS THE SAME PROTEIN WITH NO LIGANDS BOUND AND WAS USED IN MR FOR THIS STRUCTURE