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(-) Description

Title :  CRYSTAL STRUCTURE OF ORNITHINE CARBAMOYLTRANSFERASE FROM THERMUS THERMOPHILUS
 
Authors :  P. Karthe, T. S. Kumarevel, S. Kuramitsu, S. Yokoyama, Riken Structur Genomics/Proteomics Initiative (Rsgi)
Date :  19 Feb 07  (Deposition) - 13 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Ornithine Carbamoyltransferase, Ttha1199, Thermus Thermophilus, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Karthe, T. S. Kumarevel, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Ornithine Carbamoyltransferase From Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ORNITHINE CARBAMOYLTRANSFERASE
    Chains: A
    EC Number: 2.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:60BINDING SITE FOR RESIDUE MG A 302
2AC2SOFTWAREHIS A:73BINDING SITE FOR RESIDUE NA A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EF0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:261 -Pro A:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EF0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EF0)

(-) Exons   (0, 0)

(no "Exon" information available for 2EF0)

(-) 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:287
 aligned with Q5SJ15_THET8 | Q5SJ15 from UniProtKB/TrEMBL  Length:301

    Alignment length:295
                                    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     
         Q5SJ15_THET8     7 TLPKDLLDFSGYGPKELQALLDLAEQLKRERYRGEDLKGKVLALLFEKPSLRTRTTLEVAMVHLGGHAVYLDQKQVGIGEREPVRDVAKNLERFVEGIAARVFRHETVEALARHAKVPVVNALSDRAHPLQALADLLTLKEVFGGLAGLEVAWVGDGNNVLNSLLEVAPLAGLKVRVATPKGYEPDPGLLKRANAFFTHDPKEAALGAHALYTDVWTSMGQEAEREKRLRDFQGFQVNGELLKLLRPEGVFLHCLPAHYGEETTEEAVHGPRSRVFDQAENRLHTAKAVLLTLLK 301
               SCOP domains d2ef0a1 A:7-151 automated matches                                                                                                                d2ef0a2 A:152-301 automated matches                                                                                                                    SCOP domains
               CATH domains 2ef0A01 A:7-136,A:288-301  [code=3.40.50.1370, no name defined]                                                                   2ef0A02 A:137-287  [code=3.40.50.1370, no name defined]                                                                                                2ef0A01        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhh..eeeeee.hhh......hhhhhhhhhh....eeeee..hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..eee.hhhhhhh...eeee....--------hhhhhhh.....hhhhhh......eeee..........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ef0 A   7 TLPKDLLDFSGYGPKELQALLDLAEQLKRERYRGEDLKGKVLALLFEKPSLRTRTTLEVAMVHLGGHAVYLDQKQVGIGEREPVRDVAKNLERFVEGIAARVFRHETVEALARHAKVPVVNALSDRAHPLQALADLLTLKEVFGGLAGLEVAWVGDGNNVLNSLLEVAPLAGLKVRVATPKGYEPDPGLLKRANAFFTHDPKEAALGAHALYTDVWT--------EKRLRDFQGFQVNGELLKLLRPEGVFLHCLPAHYGEETTEEAVHGPRSRVFDQAENRLHTAKAVLLTLLK 301
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216      |  -     | 236       246       256       266       276       286       296     
                                                                                                                                                                                                                                                  223      232
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EF0)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5SJ15_THET8 | Q5SJ15)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0016743    carboxyl- or carbamoyltransferase activity    Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
    GO:0004585    ornithine carbamoyltransferase activity    Catalysis of the reaction: carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0006591    ornithine metabolic process    The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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