Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF T.TH. HB8 CTP SYNTHETASE
 
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 :  2.35
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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VCM)

(-) Sites  (0, 0)

(no "Site" information available for 1VCM)

(-) SS Bonds  (0, 0)

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

(-) 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 1VCM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VCM)

(-) 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:531
 aligned with PYRG_THET8 | Q5SIA8 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:539
                                    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       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539         
           PYRG_THET8    10 RPRKYVFITGGVVSSLGKGILTSSLGALLRARGYRVTAIKIDPYVNVDAGTMRPYEHGEVFVTADGAETDLDIGHYERFLDMDLSRGNNLTTGQVYLSVIQKERRGEYLSQTVQVIPHITDEIKERIRKVAEEQKAEIVVVEVGGTVGDIESLPFLEAIRQFRFDEGEGNTLYLHLTLVPYLETSEEFKTKPTQHSVATLRGVGIQPDILVLRSARPVPEEVRRKVALFTNVRPGHVFSSPTVEHLYEVPLLLEEQGLGRAVERALGLEAVIPNLSFWQEAVRVLKHPERTVKIAIAGKYVKMPDAYLSLLEALRHAGIKNRARVEVKWVDAESLEAADLDEAFRDVSGILVPGGFGVRGIEGKVRAAQYARERKIPYLGICLGLQIAVIEFARNVAGLKGANSTEFDPHTPHPVIDLMPEQLEVEGLGGTMRLGDWPMRIKPGTLLHRLYGKEEVLERHRHRYEVNPLYVDGLERAGLVVSATTPGMRGRGAGLVEAIELKDHPFFLGLQSHPEFKSRPMRPSPPFVGFVEAALAYQE 548
               SCOP domains -d1vcma2 A:11-282 CTP synthase PyrG, N-terminal domain                                                                                                                                                                                                                           ---------------d1vcma1 A:298  -547 CTP synthase PyrG, C-termi  nal domain                                                                                                                                                                                                - SCOP domains
               CATH domains 1vcmA01 A:10-296 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                          1vcmA02 A:297-  548  [code=3.40.50.880, no name   defined]                                                                                                                                                                                                   CATH domains
               Pfam domains --CTP_synth_N-1vcmA02 A:12-287                                                                                                                                                                                                                                                        -----------------------  GATase-1vcmA01 A:313-542                                                                                                                                                                                                              ------ Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhh....eeeeeee.....hhhhh........ee.....ee.hhhhhhhhhhh...hhh.eeehhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh...eeeeeeee..ee--..ee.hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhh.hhh.eeeee.....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..eeeeeeee....--...hhhhhhhhhhhhhhh.eeeeeeee....--..hhhhhh.....eee....--.hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......ee.........eeeee.hhhhh........eeeeeeeee...hhhhhhhh..eeeeeeee.eee...hhhhhhhh..eeeee...........eeeee......eeee..hhhhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vcm A  10 RPRKYVFITGGVVSSLGKGILTSSLGALLRARGYRVTAIKIDPYVNVDAGTMRPYEHGEVFVTADGAETDLDIGHYERFLDMDLSRGNNLTTGQVYLSVIQKERRGEYLSQTVQVIPHITDEIKERIRKVAEEQKAEIVVVEVGGTVGDIESLPFLEAIRQFRFDEGEGNTLYLHLTLVPYL--SEEFKTKPTQHSVATLRGVGIQPDILVLRSARPVPEEVRRKVALFTNVRPGHVFSSPTVEHLYEVPLLLEEQGLGRAVERALGLEAVIPNLSFWQEAVRVLKHPERTVKIAIAGKYV--PDAYLSLLEALRHAGIKNRARVEVKWVDAES--AADLDEAFRDVSGILVPGGF--RGIEGKVRAAQYARERKIPYLGICLGLQIAVIEFARNVAGLKGANSTEFDPHTPHPVIDLMPEQLEVEGLGGTMRLGDWPMRIKPGTLLHRLYGKEEVLERHRHRYEVNPLYVDGLERAGLVVSATTPGMRGRGAGLVEAIELKDHPFFLGLQSHPEFKSRPMRPSPPFVGFVEAALAYQE 548
                                    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       279       289       299       309|  |   319       329       339   |  |349       359     | 369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539         
                                                                                                                                                                                                               191  |                                                                                                                 310  |                           343  |                365  |                                                                                                                                                                                    
                                                                                                                                                                                                                  194                                                                                                                    313                              346                   368
   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  (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1vcm)
 
  Sites
(no "Sites" information available for 1vcm)
 
  Cis Peptide Bonds
    Ile A:125 - Pro A:126   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1vcm
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PYRG_THET8 | Q5SIA8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.3.4.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PYRG_THET8 | Q5SIA8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1vcn T.TH. HB8 CTP SYNTHETASE COMPLEX WITH SULFATE ANION
1vco T.TH. HB8 CTP SYNTHETASE COMPLEX WITH GLUTAMINE RELATED ID: TTK003000122.1 RELATED DB: TARGETDB