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(-) Description

Title :  2.00 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A CATALYTIC SUBUNIT OF AN ASPARTATE CARBAMOYLTRANSFERASE (PYRB) FROM YERSINIA PESTIS CO92
 
Authors :  A. S. Halavaty, G. Minasov, I. Dubrovska, J. Winsor, L. Shuvalova, S. Peterson, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  25 Feb 10  (Deposition) - 16 Mar 10  (Release) - 16 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Aspartate Carbamoyltransferase Catalytic Subunit, Yersinia Pestis Co92, Infectious Diseases, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Pyrimidine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, G. Minasov, I. Dubrovska, J. Winsor, L. Shuvalova, S. Peterson, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 00 Angstrom Resolution Crystal Structure Of A Catalytic Subunit Of An Aspartate Carbamoyltransferase (Pyrb) From Yersinia Pestis Co92
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ASPARTATE CARBAMOYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)CODONPLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC SUBUNIT
    Gene: PYRB, Y0161, YPO3588, YP_3842
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: ASPARTATE TRANSCARBAMYLASE, ATCASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:52 , SER A:53 , THR A:54 , ARG A:55 , THR A:56 , ARG A:106 , HIS A:135 , ARG A:230BINDING SITE FOR RESIDUE PG4 A 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LXM)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:268 -Pro A:269
2Leu B:268 -Pro B:269
3Leu C:268 -Pro C:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LXM)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_YERPE49-56
 
 		  3A:49-56
B:49-56
C:49-56

(-) Exons   (0, 0)

(no "Exon" information available for 3LXM)

(-) Sequences/Alignments

Asymmetric/Biological 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:290
 aligned with PYRB_YERPE | Q8ZB39 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:309
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
           PYRB_YERPE     2 ANPLYHKHIISINDLSRDELELVLRTAASLKKTPQPELLKHKVIASCFFEASTRTRLSFETSIHRLGASVVGFSDSSNTSLGKKGETLADTMSVISTYVDAIVMRHPQEGASRLAAQFSGNVPIVNAGDGANQHPTQTLLDLFTIQETQGRLDNINIAMVGDLKYGRTVHSLTQALAKFNGNHFFFIAPDALAMPAYILQMLEEKEIEYSLHESLEEVVPELDILYMTRVQKERLDPSEYANVKAQFILRSSDLTGARDNLKVLHPLPRIDEITTDVDKTPYAYYFQQAGNGIFARQALLALVLNAELA 310
               SCOP domains d3lxma1 A:2-151 automated matches                                                                                                                     d3lxma2 A:152-310 automated matches                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhh..eeeee..---------..hhhhhhhhhhhhh.eeeee....hhhhhhh.......eee.......hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh.....eeeee.hhhhh.hhhhhhhhhhh..eeee..hhhhhhhhh.eeee..----------hhhhhhhhh.hhhhhh......eee.........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------CARBAMOY-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxm A   2 ANPLYHKHIISINDLSRDELELVLRTAASLKKTPQPELLKHKVIASCFFEASTRTRLSFETSIHRLGASVVGFSD---------GETLADTMSVISTYVDAIVMRHPQEGASRLAAQFSGNVPIVNAGDGANQHPTQTLLDLFTIQETQGRLDNINIAMVGDLKYGRTVHSLTQALAKFNGNHFFFIAPDALAMPAYILQMLEEKEIEYSLHESLEEVVPELDILYMTR----------YANVKAQFILRSSDLTGARDNLKVLHPLPRIDEITTDVDKTPYAYYFQQAGNGIFARQALLALVLNAELA 310
                                    11        21        31        41        51        61        71    |    -    |   91       101       111       121       131       141       151       161       171       181       191       201       211       221        |-       241       251       261       271       281       291       301         
                                                                                                     76        86                                                                                                                                             230        241                                                                     


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with PYRB_YERPE | Q8ZB39 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:308
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        
           PYRB_YERPE     2 ANPLYHKHIISINDLSRDELELVLRTAASLKKTPQPELLKHKVIASCFFEASTRTRLSFETSIHRLGASVVGFSDSSNTSLGKKGETLADTMSVISTYVDAIVMRHPQEGASRLAAQFSGNVPIVNAGDGANQHPTQTLLDLFTIQETQGRLDNINIAMVGDLKYGRTVHSLTQALAKFNGNHFFFIAPDALAMPAYILQMLEEKEIEYSLHESLEEVVPELDILYMTRVQKERLDPSEYANVKAQFILRSSDLTGARDNLKVLHPLPRIDEITTDVDKTPYAYYFQQAGNGIFARQALLALVLNAEL 309
               SCOP domains d3lxmb1 B:2-151 automated matches                                                                                                                     d3lxmb2 B:152-309 automated matches                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhh..eeeee...----------hhhhhhhhhh....eeeeee...hhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh.....eeeee.hhhhh.hhhhhhhhhhh..eeeee..hhhhhhhh.eeee..----------------....hhhhhh......eee.........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------CARBAMOY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxm B   2 ANPLYHKHIISINDLSRDELELVLRTAASLKKTPQPELLKHKVIASCFFEASTRTRLSFETSIHRLGASVVGFSDS----------TLADTMSVISTYVDAIVMRHPQEGASRLAAQFSGNVPIVNAGDGANQHPTQTLLDLFTIQETQGRLDNINIAMVGDLKYGRTVHSLTQALAKFNGNHFFFIAPDALAMPAYILQMLEEKEIEYSLHESLEEVVPELDILYMTR----------------QFILRSSDLTGARDNLKVLHPLPRIDEITTDVDKTPYAYYFQQAGNGIFARQALLALVLNAEL 309
                                    11        21        31        41        51        61        71     |   -      | 91       101       111       121       131       141       151       161       171       181       191       201       211       221        |-         -     | 251       261       271       281       291       301        
                                                                                                      77         88                                                                                                                                           230              247                                                              


Chain C from PDB  Type:PROTEIN  Length:277
 aligned with PYRB_YERPE | Q8ZB39 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:306
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302      
           PYRB_YERPE     3 NPLYHKHIISINDLSRDELELVLRTAASLKKTPQPELLKHKVIASCFFEASTRTRLSFETSIHRLGASVVGFSDSSNTSLGKKGETLADTMSVISTYVDAIVMRHPQEGASRLAAQFSGNVPIVNAGDGANQHPTQTLLDLFTIQETQGRLDNINIAMVGDLKYGRTVHSLTQALAKFNGNHFFFIAPDALAMPAYILQMLEEKEIEYSLHESLEEVVPELDILYMTRVQKERLDPSEYANVKAQFILRSSDLTGARDNLKVLHPLPRIDEITTDVDKTPYAYYFQQAGNGIFARQALLALVLNAE 308
               SCOP domains d3lxmc1 C:3-151 automated matches                                                                                                                    d3lxmc2 C:152-308 automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----OTCace_N-3lxmC04 C:8-149                                                                                                                      ----OTCace-3lxmC01 C:154-304                                                                                                                               ---- Pfam domains (1)
           Pfam domains (2) -----OTCace_N-3lxmC05 C:8-149                                                                                                                      ----OTCace-3lxmC02 C:154-304                                                                                                                               ---- Pfam domains (2)
           Pfam domains (3) -----OTCace_N-3lxmC06 C:8-149                                                                                                                      ----OTCace-3lxmC03 C:154-304                                                                                                                               ---- Pfam domains (3)
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhh..eeeee...--------..hhhhhhhhhhhhh.eeeeee...hhhhhhhhhh....eeeeee...--.hhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh.....eeeee.hhhhh.hhhhhhhhhhh...eeee.....hhhhh.eeee.-------------------..hhhhhh......eee..........hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------CARBAMOY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lxm C   3 NPLYHKHIISINDLSRDELELVLRTAASLKKTPQPELLKHKVIASCFFEASTRTRLSFETSIHRLGASVVGFSDS--------GETLADTMSVISTYVDAIVMRHPQEGASRLAAQFSGNVPIVNAGDGAN--PTQTLLDLFTIQETQGRLDNINIAMVGDLKYGRTVHSLTQALAKFNGNHFFFIAPDALAMPAYILQMLEEKEIEYSLHESLEEVVPELDILYMT-------------------ILRSSDLTGARDNLKVLHPLPRIDEITTDVDKTPYAYYFQQAGNGIFARQALLALVLNAE 308
                                    12        22        32        42        52        62        72    |    -   |    92       102       112       122       132|  |   142       152       162       172       182       192       202       212       222      |  -         -      |252       262       272       282       292       302      
                                                                                                     77       86                                            133  |                                                                                          229                 249                                                           
                                                                                                                                                               136
   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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LXM)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: OTCace] (48)
(-)
Family: OTCace (48)
(-)
Yersinia pestis (1)
1aOTCace-3lxmC01C:154-304
1bOTCace-3lxmC02C:154-304
1cOTCace-3lxmC03C:154-304
(-)
Clan: no clan defined [family: OTCace_N] (48)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (PYRB_YERPE | Q8ZB39)
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:0004070    aspartate carbamoyltransferase activity    Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
    GO:0016743    carboxyl- or carbamoyltransferase activity    Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
    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:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    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: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:0009220    pyrimidine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0000050    urea cycle    The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
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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 Related Entries

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