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(-) Description

Title :  CRYSTAL STRUCTURE OF T.TH. HB8 CTP SYNTHETASE COMPLEX WITH SULFATE ANION
 
Authors :  M. Goto, Riken Structural Genomics/Proteomics Initiative (Rsgi
Date :  10 Mar 04  (Deposition) - 31 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Tetramer, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Goto, R. Omi, N. Nakagawa, I. Miyahara, K. Hirotsu
Crystal Structures Of Ctp Synthetase Reveal Atp, Utp, And Glutamine Binding Sites
Structure V. 12 1413 2004
PubMed-ID: 15296735  |  Reference-DOI: 10.1016/J.STR.2004.05.013

(-) Compounds

Molecule 1 - CTP SYNTHETASE
    Chains: A
    EC Number: 6.3.4.2
    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: HB8
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:27 , LYS A:49 , GLU A:151 , GLY A:153 , GLY A:154 , HOH A:644 , HOH A:873BINDING SITE FOR RESIDUE SO4 A 610
2AC2SOFTWARESER A:24 , LEU A:25 , GLY A:26 , LYS A:27 , GLY A:28 , HOH A:637 , HOH A:638 , HOH A:648BINDING SITE FOR RESIDUE SO4 A 620
3AC3SOFTWARELYS A:198 , THR A:199 , LYS A:200 , LYS A:234 , HOH A:662 , HOH A:719BINDING SITE FOR RESIDUE SO4 A 630

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:125 -Pro A:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VCN)

(-) 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:506
 aligned with PYRG_THET8 | Q5SIA8 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:537
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       
           PYRG_THET8    11 PRKYVFITGGVVSSLGKGILTSSLGALLRARGYRVTAIKIDPYVNVDAGTMRPYEHGEVFVTADGAETDLDIGHYERFLDMDLSRGNNLTTGQVYLSVIQKERRGEYLSQTVQVIPHITDEIKERIRKVAEEQKAEIVVVEVGGTVGDIESLPFLEAIRQFRFDEGEGNTLYLHLTLVPYLETSEEFKTKPTQHSVATLRGVGIQPDILVLRSARPVPEEVRRKVALFTNVRPGHVFSSPTVEHLYEVPLLLEEQGLGRAVERALGLEAVIPNLSFWQEAVRVLKHPERTVKIAIAGKYVKMPDAYLSLLEALRHAGIKNRARVEVKWVDAESLEAADLDEAFRDVSGILVPGGFGVRGIEGKVRAAQYARERKIPYLGICLGLQIAVIEFARNVAGLKGANSTEFDPHTPHPVIDLMPEQLEVEGLGGTMRLGDWPMRIKPGTLLHRLYGKEEVLERHRHRYEVNPLYVDGLERAGLVVSATTPGMRGRGAGLVEAIELKDHPFFLGLQSHPEFKSRPMRPSPPFVGFVEAALAYQ 547
               SCOP domains d1vcna2 A:11-282 CTP synthase PyrG, N-terminal doma     in                                                                                                                                                                                                                      ------------ --d1vcna1 A:2    98-547 CTP synthase PyrG, C-t    erminal domain                                                                                                                                                                                             SCOP domains
               CATH domains 1vcnA01 A:11-296 P-loop containing nucleotide triph     osphate hydrolases                                                                                                                                                                                                                    1vcnA02 A:29    7-547  [code=3.40.50.880, no     name defined]                                                                                                                                                                                              CATH domains
               Pfam domains -CTP_synth_N-1vcnA02 A:12-287                                                                                                                                                                                                                                                        ------- -------------    GATase-1vcnA01 A:313-542                                                                                                                                                                                                              ----- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhhhh....eeeeeee..........-----...ee.....ee.hhhhhhhhhhh...hhh.eeehhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeee..ee....ee.hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhh...hhh.eee....-..hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh-...eeeeeeee..----hhhhhhhhhhhhhhhhhh.eeeeeeee..----..hhhhhh.....eee...--...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......ee.........eeeeee-----------eeeeeeeeeee...hhhhhhhh..eeeeeeeeeeee...hhhhhhhh..eeeee....---....eeeee......eeee..hhhhhh.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vcn A  11 PRKYVFITGGVVSSLGKGILTSSLGALLRARGYRVTAIKIDPYVNVDAGTM-----GEVFVTADGAETDLDIGHYERFLDMDLSRGNNLTTGQVYLSVIQKERRGEYLSQTVQVIPHITDEIKERIRKVAEEQKAEIVVVEVGGTVGDIESLPFLEAIRQFRFDEGEGNTLYLHLTLVPYLETSEEFKTKPTQHSVATLRGVGIQPDILVLRSARPVPEEVRRKVALFTNVRPGHVFSSPTV-HLYEVPLLLEEQGLGRAVERALGLEAVIPNLSFWQEAVRVL-HPERTVKIAIAGK----PDAYLSLLEALRHAGIKNRARVEVKWVDA----AADLDEAFRDVSGILVPGG--VRGIEGKVRAAQYARERKIPYLGICLGLQIAVIEFARNVAGLKGANSTEFDPHTPHPVIDLM-----------TMRLGDWPMRIKPGTLLHRLYGKEEVLERHRHRYEVNPLYVDGLERAGLVVSATTPGM---GAGLVEAIELKDHPFFLGLQSHPEFKSRPMRPSPPFVGFVEAALAYQ 547
                                    20        30        40        50        60|     | 70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 | |   260       270       280       290   | | 300       | -  |    320       330       340|    | 350       360   |  |370       380       390       400       410       420       | -       440       450       460       470       480       490      |  -|      510       520       530       540       
                                                                             61    67                                                                                                                                                                                      252 |                                     294 |         308  313                         341  346               364  |                                                          428         440                                                      497 501                                              
                                                                                                                                                                                                                                                                             254                                       296                                                                    367
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Glutaminase_I (73)
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (PYRG_THET8 | Q5SIA8)
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:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    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.

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 Related Entries

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UniProtKB/Swiss-Prot
        PYRG_THET8 | Q5SIA8: 1vcm 1vco

(-) Related Entries Specified in the PDB File

1vcm NATIVE T.TH. HB8 CTP SYNTHETASE
1vco T.TH. HB8 CTP SYNTHETASE COMPLEX WITH GLUTAMINE RELATED ID: TTK003000122.2 RELATED DB: TARGETDB