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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SYNTHETASE DOMAIN OF HUMAN CTP SYNTHETASE
 
Authors :  P. Stenmark, P. Kursula, C. Arrowsmith, H. Berglund, A. Edwards, M. Ehn S. Flodin, S. Graslund, M. Hammarstrom, B. M. Hallberg, L. Holmberg-S T. Kotenyoa, M. Moche, P. Nilsson-Ehle, D. Ogg, C. Persson, J. Sagemar H. Schuler, M. Sundstrom, A. G. Thorsell, S. Van Den Berg, J. Weigelt P. Nordlund
Date :  08 Feb 08  (Deposition) - 11 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Pyrimidine Biosynthesis, Glutamine Amidotransferase, Phosphorylation, Amidotransferase, Cytidine 5-Prime Triphosphate Synthetase, Ctp, Utp, Ctps, Ligase, Glutamine, Ctp Synthase, Phosphoprotein, Ctp Synthetase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kursula, S. Flodin, M. Ehn, M. Hammarstrom, H. Schuler, P. Nordlund P. Stenmark
Structure Of The Synthetase Domain Of Human Ctp Synthetase, A Target For Anticancer Therapy.
Acta Crystallogr. , Sect. F V. 62 613 2006
PubMed-ID: 16820675  |  Reference-DOI: 10.1107/S1744309106018136

(-) Compounds

Molecule 1 - CTP SYNTHASE 1
    Chains: A, B
    EC Number: 6.3.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PG-TF2 (TAKARA)
    Expression System Strain: BL21(DE3)-GOLD
    Expression System Taxid: 469008
    Expression System Vector: PNIC-BSA4
    Fragment: SYNTHETASE DOMAIN, RESIDUES 1-273
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: DISULFIDE LINK BETWEEN B218 AND B243
    Synonym: CTP SYNTHETASE, UTP--AMMONIA LIGASE 1, CTP SYNTHETASE 1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , ILE A:14 , GLY A:15 , LYS A:16 , GLY A:17 , SO4 A:1275BINDING SITE FOR RESIDUE SO4 A1273
2AC2SOFTWARELYS A:193 , THR A:194 , LYS A:195 , LYS A:229BINDING SITE FOR RESIDUE SO4 A1274
3AC3SOFTWARESER A:12 , GLY A:13 , LYS A:16 , TYR A:42 , GLY A:148 , GLY A:149 , SO4 A:1273BINDING SITE FOR RESIDUE SO4 A1275
4AC4SOFTWAREGLY B:13 , ILE B:14 , GLY B:15 , LYS B:16 , GLY B:17BINDING SITE FOR RESIDUE SO4 B1273
5AC5SOFTWARESER A:12 , LYS B:193 , THR B:194 , LYS B:195BINDING SITE FOR RESIDUE SO4 B1274

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:218 -B:243

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:85 -Asn A:86
2Val A:114 -Pro A:115
3Val B:114 -Pro B:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VO1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VO1)

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003726211ENSE00001458274chr1:41445007-41445501495PYRG1_HUMAN-00--
1.5cENST000003726215cENSE00002144581chr1:41448950-41449128179PYRG1_HUMAN1-56562A:1-45
B:1-46		45
46
1.6bENST000003726216bENSE00001123011chr1:41450493-41450663171PYRG1_HUMAN56-113582A:85-113
B:87-113		29
27
1.7ENST000003726217ENSE00001190755chr1:41453044-41453144101PYRG1_HUMAN113-146342A:113-146
B:113-146 (gaps)		34
34
1.8cENST000003726218cENSE00001190751chr1:41454266-41454382117PYRG1_HUMAN147-185392A:147-185
B:147-185		39
39
1.9ENST000003726219ENSE00001190748chr1:41456837-4145692084PYRG1_HUMAN186-213282A:186-213 (gaps)
B:186-213 (gaps)		28
28
1.10cENST0000037262110cENSE00001190744chr1:41457437-4145751781PYRG1_HUMAN214-240272A:214-240
B:214-240		27
27
1.11bENST0000037262111bENSE00001190740chr1:41461589-41461740152PYRG1_HUMAN241-291512A:241-273
B:241-273		33
33
1.12bENST0000037262112bENSE00001226457chr1:41463066-41463198133PYRG1_HUMAN291-335450--
1.13cENST0000037262113cENSE00001190726chr1:41466701-4146678989PYRG1_HUMAN336-365300--
1.15bENST0000037262115bENSE00001190724chr1:41467832-4146792695PYRG1_HUMAN365-397330--
1.16aENST0000037262116aENSE00001190721chr1:41468786-4146884863PYRG1_HUMAN397-418220--
1.18aENST0000037262118aENSE00001190718chr1:41471723-4147176644PYRG1_HUMAN418-432150--
1.19ENST0000037262119ENSE00001123002chr1:41473121-4147321797PYRG1_HUMAN433-465330--
1.20aENST0000037262120aENSE00001122991chr1:41474331-4147438656PYRG1_HUMAN465-483190--
1.20cENST0000037262120cENSE00001122982chr1:41474466-4147456297PYRG1_HUMAN484-516330--
1.21ENST0000037262121ENSE00001122971chr1:41475117-41475261145PYRG1_HUMAN516-564490--
1.22ENST0000037262122ENSE00001190765chr1:41475833-4147592694PYRG1_HUMAN564-591280--
1.23cENST0000037262123cENSE00001458238chr1:41477330-41478235906PYRG1_HUMAN-00--

(-) 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:235
 aligned with PYRG1_HUMAN | P17812 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:275
                              1                                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268     
          PYRG1_HUMAN     - --MKYILVTGGVISGIGKGIIASSVGTILKSCGLHVTSIKIDPYINIDAGTFSPYEHGEVFVLDDGGEVDLDLGNYERFLDIRLTKDNNLTTGKIYQYVINKERKGDYLGKTVQVVPHITDAIQEWVMRQALIPVDEDGLEPQVCVIELGGTVGDIESMPFIEAFRQFQFKVKRENFCNIHVSLVPQPSSTGEQKTKPTQNSVRELRGLGLSPDLVVCRCSNPLDTSVKEKISMFCHVEPEQVICVHDVSSIYRVPLLLEEQGVVDYFLRRLDLP 273
               SCOP domains --d2vo1a1 A:1-273 CTP synthase PyrG, N-terminal                                        domain                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhhh...eeeeeee.....---------------------------------------..eeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..........eeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeeeee......-....hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..hhh.eeee....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.5c  PDB: A:1-45 UniProt: 1-56 [INCOMPLETE]       --------------------------------------------------------Exon 1.7  PDB: A:113-146          Exon 1.8c  PDB: A:147-185              Exon 1.9 UniProt: 186-213   Exon 1.10c  PDB: A:214-240 Exon 1.11b  PDB: A:241-273        Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.6b  PDB: A:85-113 UniProt: 56-113 [INCOMPLETE]     ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2vo1 A  -1 QSMKYILVTGGVISGIGKGIIASSVGTILKSCGLHVTSIKIDPYINI---------------------------------------DNNLTTGKIYQYVINKERKGDYLGKTVQVVPHITDAIQEWVMRQALIPVDEDGLEPQVCVIELGGTVGDIESMPFIEAFRQFQFKVKRENFCNIHVSLVPQPSS-GEQKTKPTQNSVRELRGLGLSPDLVVCRCSNPLDTSVKEKISMFCHVEPEQVICVHDVSSIYRVPLLLEEQGVVDYFLRRLDLP 273
                                     8        18        28        38      |  -         -         -         -      | 88        98       108       118       128       138       148       158       168       178       188 |     198       208       218       228       238       248       258       268     
                                                                         45                                      85                                                                                                    188 |                                                                                   
                                                                                                                                                                                                                         190                                                                                   


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with PYRG1_HUMAN | P17812 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:274
                             1                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    
          PYRG1_HUMAN     - -MKYILVTGGVISGIGKGIIASSVGTILKSCGLHVTSIKIDPYINIDAGTFSPYEHGEVFVLDDGGEVDLDLGNYERFLDIRLTKDNNLTTGKIYQYVINKERKGDYLGKTVQVVPHITDAIQEWVMRQALIPVDEDGLEPQVCVIELGGTVGDIESMPFIEAFRQFQFKVKRENFCNIHVSLVPQPSSTGEQKTKPTQNSVRELRGLGLSPDLVVCRCSNPLDTSVKEKISMFCHVEPEQVICVHDVSSIYRVPLLLEEQGVVDYFLRRLDLP 273
               SCOP domains d2vo1b_ B: CTP synthase PyrG, N-terminal domain                                                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhhhh....eeeeeee......----------------------------------------.eehhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh..----.....eeeeee........hhhhhhhhhhhhhhhhhh.eeeeeeee.....--....hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhh.hhh.eeee......hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -Exon 1.5c  PDB: B:1-46 UniProt: 1-56 [INCOMPLETE]       --------------------------------------------------------Exon 1.7  PDB: B:113-146 (gaps)   Exon 1.8c  PDB: B:147-185              Exon 1.9 UniProt: 186-213   Exon 1.10c  PDB: B:214-240 Exon 1.11b  PDB: B:241-273        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.6b  PDB: B:87-113 UniProt: 56-113 [INCOMPLETE]     ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2vo1 B   0 SMKYILVTGGVISGIGKGIIASSVGTILKSCGLHVTSIKIDPYINID----------------------------------------NLTTGKIYQYVINKERKGDYLGKTVQVVPHITDAIQEWVMRQALIP----GLEPQVCVIELGGTVGDIESMPFIEAFRQFQFKVKRENFCNIHVSLVPQPS--GEQKTKPTQNSVRELRGLGLSPDLVVCRCSNPLDTSVKEKISMFCHVEPEQVICVHDVSSIYRVPLLLEEQGVVDYFLRRLDLP 273
                                     9        19        29        39      |  -         -         -         -       |89        99       109       119       129  |    139       149       159       169       179       | -|      199       209       219       229       239       249       259       269    
                                                                         46                                       87                                          132  137                                               187  |                                                                                   
                                                                                                                                                                                                                        190
   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  (0, 0)

(no "CATH Domain" information available for 2VO1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VO1)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PYRG1_HUMAN | P17812)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003883    CTP synthase activity    Catalysis of the reaction: ATP + UTP + NH3 = ADP + phosphate + CTP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0044210    'de novo' CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of cytidine 5'-triphosphate (CTP) from simpler components.
    GO:0042100    B cell proliferation    The expansion of a B cell population by cell division. Follows B cell activation.
    GO:0006241    CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
    GO:0042098    T cell proliferation    The expansion of a T cell population by cell division. Follows T cell activation.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRG1_HUMAN | P17812: 5u03

(-) Related Entries Specified in the PDB File

2c5m CRYSTAL STRUCTURE OF THE SYNTHETASE DOMAIN OF HUMAN CTP SYNTHETASE