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(-) Description

Title :  CRYSTAL STRUCTURE OF UNLIGANDED ASPARTATE TRANSCARBAMOYLASE FROM BACILLUS SUBTILIS
 
Authors :  D. E. Puleo, K. M. Harris, G. M. Cockrell, E. R. Kantrowitz
Date :  22 Mar 11  (Deposition) - 08 Jun 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Aspartate Transcarbamoylase, Transferase, Catalytic Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Harris, G. M. Cockrell, D. E. Puleo, E. R. Kantrowitz
Crystallographic Snapshots Of The Complete Catalytic Cycle Of The Unregulated Aspartate Transcarbamoylase From Bacillu Subtilis.
J. Mol. Biol. V. 411 190 2011
PubMed-ID: 21663747  |  Reference-DOI: 10.1016/J.JMB.2011.05.036

(-) Compounds

Molecule 1 - ASPARTATE CARBAMOYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYRB, BSU15490
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    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, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:67 , HOH A:319 , HOH A:323 , HOH A:328 , HOH A:334 , HOH A:367 , HOH A:385 , HOH A:388 , HOH A:411 , ASN B:67 , HOH B:313 , ASN C:67BINDING SITE FOR RESIDUE PO4 A 305
2AC2SOFTWARESER A:11 , THR A:12 , ARG A:171 , HOH A:312 , HOH A:343BINDING SITE FOR RESIDUE PO4 A 306
3AC3SOFTWARETHR A:73 , SER A:74 , LYS A:77 , SER C:47 , THR C:48 , ARG C:49 , PRO C:251BINDING SITE FOR RESIDUE PO4 A 307
4AC4SOFTWARESER B:11 , THR B:12 , ARG B:171 , HOH B:372 , HOH B:484BINDING SITE FOR RESIDUE PO4 B 305
5AC5SOFTWARELYS C:272 , LYS C:275 , HOH C:357 , HOH C:381BINDING SITE FOR RESIDUE PO4 C 305
6AC6SOFTWARESER C:11 , THR C:12 , ARG C:171 , HOH C:359 , HOH C:573BINDING SITE FOR RESIDUE PO4 C 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R7D)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:250 -Pro A:251
2Ala B:250 -Pro B:251
3Ala C:250 -Pro C:251

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R7D)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_BACSU43-50
 
 		  3A:43-50
B:43-50
C:43-50

(-) Exons   (0, 0)

(no "Exon" information available for 3R7D)

(-) 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:291
 aligned with PYRB_BACSU | P05654 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:291
                                    10        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 
           PYRB_BACSU     1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
               SCOP domains d3r7da1 A:1-143 automated matches                                                                                                              d3r7da2 A:144-291 automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhh..eeeeee..hhhhhh..hhhhhhhhhhhh...eeeee.....hhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh..eeeee.hhhhh.......ee.hhhhhhhhh.eeee.........hhhhhhhhhhhhh.hhhhhh......eee...........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CARBAMOY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r7d A   1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
                                    10        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 


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with PYRB_BACSU | P05654 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:291
                                    10        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 
           PYRB_BACSU     1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
               SCOP domains d3r7db1 B:1-143 automated matches                                                                                                              d3r7db2 B:144-291 automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhhhhh..eeeeee..hhhhhh..hhhhhhhhhhhhh..eeeee.....hhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh..eeeee.hhhhh......eee.hhhhhhhhh.eeee...............hhhhhhh.hhhhhh......eee...........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CARBAMOY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r7d B   1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
                                    10        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 


Chain C from PDB  Type:PROTEIN  Length:291
 aligned with PYRB_BACSU | P05654 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:291
                                    10        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 
           PYRB_BACSU     1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
               SCOP domains d3r7dc1 C:1-143 automated matches                                                                                                              d3r7dc2 C:144-291 automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -OTCace_N-3r7dC04 C:2-141                                                                                                                    ----OTCace-3r7dC01 C:146-288                                                                                                                       --- Pfam domains (1)
           Pfam domains (2) -OTCace_N-3r7dC05 C:2-141                                                                                                                    ----OTCace-3r7dC02 C:146-288                                                                                                                       --- Pfam domains (2)
           Pfam domains (3) -OTCace_N-3r7dC06 C:2-141                                                                                                                    ----OTCace-3r7dC03 C:146-288                                                                                                                       --- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhhhhh..eeeeee..hhhhhh..hhhhhhhhhhhhh..eeeee.....hhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh..eeeee.hhhhh.......ee.hhhhhhhhh.eeee............hhhhhhhhhh.hhhhhhh.....eee...........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CARBAMOY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r7d C   1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
                                    10        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
   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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R7D)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: OTCace] (48)
(-)
Family: OTCace (48)
(-)
Bacillus subtilis (3)
1aOTCace-3r7dC01C:146-288
1bOTCace-3r7dC02C:146-288
1cOTCace-3r7dC03C:146-288
(-)
Clan: no clan defined [family: OTCace_N] (48)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (PYRB_BACSU | P05654)
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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  3r7d
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRB_BACSU | P05654: 2at2 3r7f 3r7l

(-) Related Entries Specified in the PDB File

3r7f 3r7l