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(-) Description

Title :  CRYSTAL STRUCTURE OF THE M. TUBERCULOSIS CTP SYNTHASE PYRG IN COMPLEX WITH UTP, AMP-PCP AND OXONORLEUCINE
 
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 :  3.49
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (2x),B (2x)
Biol. Unit 2:  A (2x),B (2x)
Keywords :  Ctp Synthase, Pyrg, Amidotransferase, Utp, Amp-Pcp, 5-Oxo-L- Norleucine, 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, B
    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

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3ONL2Ligand/Ion5-OXO-L-NORLEUCINE
4UTP2Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3ONL2Ligand/Ion5-OXO-L-NORLEUCINE
4UTP2Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3ONL2Ligand/Ion5-OXO-L-NORLEUCINE
4UTP2Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:365 , GLY A:366 , PHE A:367 , CYS A:393 , GLN A:397 , GLU A:416 , ARG A:475 , HIS A:476 , ARG A:477 , TYR A:478binding site for residue ONL A 601
2AC2SOFTWARESER A:21 , LEU A:22 , GLY A:23 , LYS A:24 , GLY A:25 , LEU A:26 , LYS A:46 , ASP A:78 , GLU A:152 , ARG A:223 , ASP A:252 , ALA A:253 , ILE A:256 , ILE A:259 , MG A:604 , PRO B:194binding site for residue ACP A 602
3AC3SOFTWARESER A:20 , GLN A:120 , ILE A:122 , ASP A:159 , ILE A:160 , GLU A:161 , LEU B:198 , LYS B:199 , THR B:200 , LYS B:201 , GLN B:204binding site for residue UTP A 603
4AC4SOFTWAREGLY A:25 , ASP A:78 , GLU A:152 , ACP A:602binding site for residue MG A 604
5AC5SOFTWAREPRO A:194 , SER B:21 , LEU B:22 , GLY B:23 , LYS B:24 , GLY B:25 , LEU B:26 , LYS B:46 , ASP B:78 , GLU B:152 , ARG B:223 , ALA B:253 , ILE B:259 , MG B:604binding site for residue ACP B 602
6AC6SOFTWARELYS A:199 , THR A:200 , LYS A:201 , GLN A:204 , SER B:20 , GLN B:120 , ILE B:122 , ASP B:159 , ILE B:160 , GLU B:161binding site for residue UTP B 603
7AC7SOFTWAREGLY B:25 , ASP B:78 , GLU B:152 , ACP B:602binding site for residue MG B 604
8AC8SOFTWAREGLY B:365 , GLY B:366 , LEU B:392 , LEU B:394 , GLY B:395 , LEU B:396 , GLN B:397 , GLU B:416 , ARG B:475 , HIS B:476 , ARG B:477 , TYR B:478 , THR B:521 , GLN B:522 , ALA B:523 , HIS B:524binding site for Di-peptide ONL B 601 and CYS B 393

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:122 -Pro A:123
2Ile B:122 -Pro B:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZDK)

(-) 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:534
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhh.eee.....eeehhhhhhhhhhh...hhh.eeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.........eeeeee........hhhhhhhhhhhhhhhh...eeeeeeee..ee....ee.hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhh.hhh.eeeee...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh.....ee.........eeeee.....eeeeeeeee...hhhhhhhh..eeeeeeee.eee...hhhhhhhhh.eeeee......eeeee........eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zdk A   7 TATKHLFVSGGVASSLGKGLTASSLGQLLTARGLHVTMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDVGHYERFLDRNLPGSANVTTGQVYSTVIAKERRGEYLGDTVQVIPHITDEIKRRILAMAQPDADGNRPDVVITEIGGTVGDIESQPFLEAARQVRHYLGREDVFFLHVSLVPYLAPSGELKTKPTQHSVAALRSIGITPDALILRCDRDVPEALKNKIALMCDVDIDGVISTPDAPSIYDIPKVLHREELDAFVVRRLNLPFRDVDWTEWDDLLRRVHEPHETVRIALVGKYVELSDAYLSVAEALRAGGFKHRAKVEICWVASDGCETTSGAAAALGDVHGVLIPGGFGIRGIEGKIGAIAYARARGLPVLGLCLGLQCIVIEAARSVGLTNANSAEFDPDTPDPVIATMGGTMRLGSYPAVLEPDSVVAQAYQTTQVSERHRHRYEVNNAYRDKIAESGLRFSGTSPDGHLVEFVEYPPDRHPFVVGTQAHPELKSRPTRPHPLFVAFVGAAIDYKAGEL 553
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426  ||   449       459       469       479       489       499       509       519       529       539       549    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                429|                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 443                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:534
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhh.eee.....eeehhhhhhhhhhh...hhh.eeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.........eeeeee........hhhhhhhhhhhhhhhh...eeeeeeee..ee....ee.hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhh.hhh.eeeee...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..eeeeeeeee.....hhhhhhhhhhhhhhhhhh.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
                 4zdk B   7 TATKHLFVSGGVASSLGKGLTASSLGQLLTARGLHVTMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDVGHYERFLDRNLPGSANVTTGQVYSTVIAKERRGEYLGDTVQVIPHITDEIKRRILAMAQPDADGNRPDVVITEIGGTVGDIESQPFLEAARQVRHYLGREDVFFLHVSLVPYLAPSGELKTKPTQHSVAALRSIGITPDALILRCDRDVPEALKNKIALMCDVDIDGVISTPDAPSIYDIPKVLHREELDAFVVRRLNLPFRDVDWTEWDDLLRRVHEPHETVRIALVGKYVELSDAYLSVAEALRAGGFKHRAKVEICWVASDGCETTSGAAAALGDVHGVLIPGGFGIRGIEGKIGAIAYARARGLPVLGLCLGLQCIVIEAARSVGLTNANSAEFDPDTPDPVIATMGGTMRLGSYPAVLEPDSVVAQAYQTTQVSERHRHRYEVNNAYRDKIAESGLRFSGTSPDGHLVEFVEYPPDRHPFVVGTQAHPELKSRPTRPHPLFVAFVGAAIDYKAGEL 553
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426  ||   449       459       469       479       489       499       509       519       529       539       549    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                429|                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 443
   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  (0, 0)

(no "SCOP Domain" information available for 4ZDK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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        PYRG_MYCTU | P9WHK7: 4zdi 4zdj

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