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(-) Description

Title :  CRYSTAL STRUCTURE OF THE M. TUBERCULOSIS CTP SYNTHASE PYRG IN COMPLEX WITH TWO UTP MOLECULES
 
Authors :  M. Bellinzoni, N. Barilone, P. M. Alzari
Date :  17 Apr 15  (Deposition) - 01 Jul 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Ctp Synthase, Pyrg, Amidotransferase, Utp, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Mori, L. R. Chiarelli, M. Esposito, V. Makarov, M. Bellinzoni, R. C. Hartkoorn, G. Degiacomi, F. Boldrin, S. Ekins, A. L. De Jesus Lopes Ribeiro, L. B. Marino, I. Centarova, Z. Svetlikova, J. Blasko, E. Kazakova, A. Lepioshkin, N. Barilone, G. Zanoni, A. Porta, M. Fondi, R. Fani, A. R. Baulard, K. Mikusova, P. M. Alzari, R. Manganelli, L. P. De Carvalho, G. Riccardi, S. T. Cole M. R. Pasca
Thiophenecarboxamide Derivatives Activated By Etha Kill Mycobacterium Tuberculosis By Inhibiting The Ctp Synthetase Pyrg.
Chem. Biol. V. 22 917 2015
PubMed-ID: 26097035  |  Reference-DOI: 10.1016/J.CHEMBIOL.2015.05.016

(-) Compounds

Molecule 1 - CTP SYNTHASE
    Chains: A
    EC Number: 6.3.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A
    Expression System Taxid: 469008
    Gene: PYRG, RV1699, MTCI125.21
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Synonym: CTP SYNTHETASE,UTP--AMMONIA LIGASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
3UTP2Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3UTP8Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:20 , GLN A:120 , VAL A:121 , ILE A:122 , ASP A:159 , ILE A:160 , GLU A:161 , LYS A:199 , THR A:200 , LYS A:201 , GLN A:204 , LYS A:235 , MG A:603 , HOH A:715 , HOH A:737 , HOH A:756 , HOH A:801 , HOH A:812 , HOH A:835 , HOH A:850 , HOH A:884binding site for residue UTP A 601
2AC2SOFTWARESER A:21 , LEU A:22 , GLY A:23 , LYS A:24 , LEU A:26 , THR A:27 , PRO A:194 , ARG A:223 , THR A:250 , ASP A:252 , ALA A:253 , ILE A:256 , ILE A:259 , MG A:604 , HOH A:701 , HOH A:702 , HOH A:703 , HOH A:722 , HOH A:732 , HOH A:745 , HOH A:778 , HOH A:781 , HOH A:798 , HOH A:819 , HOH A:901binding site for residue UTP A 602
3AC3SOFTWAREUTP A:601 , HOH A:801 , HOH A:850 , HOH A:884binding site for residue MG A 603
4AC4SOFTWAREUTP A:602 , HOH A:701 , HOH A:702 , HOH A:722 , HOH A:901binding site for residue MG A 604
5AC5SOFTWAREPRO A:60 , PHE A:61 , ALA A:316 , TYR A:317 , GLY A:365 , PHE A:367 , HOH A:750 , HOH A:791binding site for residue GOL A 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:122 -Pro A:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZDJ)

(-) 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:535
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee......hhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhh..ee.....ee.hhhhhhhhhhh...hhh.eeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...........eeeeee........hhhhhhhhhhhhhhhh...eeeeeeee..ee....ee.hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhh.hhh.eeeee...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh.....ee.........eeeee.....eeeeeeeee...hhhhhhhh..eeeeeeee.eee...hhhhhhhhh.eeeee......eeeee........eeee..hhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zdj A   5 PQTATKHLFVSGGVASSLGKGLTASSLGQLLTARGLHVTMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDVGHYERFLDRNLPGSANVTTGQVYSTVIAKERRGEYLGDTVQVIPHITDEIKRRILAMAQPDADGNRPDVVITEIGGTVGDIESQPFLEAARQVRHYLGREDVFFLHVSLVPYLAPSGELKTKPTQHSVAALRSIGITPDALILRCDRDVPEALKNKIALMCDVDIDGVISTPDAPSIYDIPKVLHREELDAFVVRRLNLPFRDVDWTEWDDLLRRVHEPHETVRIALVGKYVELSDAYLSVAEALRAGGFKHRAKVEICWVASDGCETTSGAAAALGDVHGVLIPGGFGIRGIEGKIGAIAYARARGLPVLGLCLGLQCIVIEAARSVGLTNANSAEFDPDTPDPVIATMGGTMRLGSYPAVLEPDSVVAQAYQTTQVSERHRHRYEVNNAYRDKIAESGLRFSGTSPDGHLVEFVEYPPDRHPFVVGTQAHPELKSRPTRPHPLFVAFVGAAIDYKAGE 552
                                    14        24        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       334       344       354       364       374       384       394       404       414       424    || 447       457       467       477       487       497       507       517       527       537       547     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  429|                                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   443
   Legend:   → Mismatch (orange background)
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  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 4ZDJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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    Ile A:122 - Pro A:123   [ RasMol ]  
 
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  4zdj
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  PYRG_MYCTU | P9WHK7
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  6.3.4.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRG_MYCTU | P9WHK7: 4zdi 4zdk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZDJ)