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(-) Description

Title :  CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY
 
Authors :  R. P. Kosman, J. E. Gouaux, W. N. Lipscomb
Date :  14 Aug 92  (Deposition) - 31 Jan 94  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Kosman, J. E. Gouaux, W. N. Lipscomb
Crystal Structure Of Ctp-Ligated T State Aspartate Transcarbamoylase At 2. 5 A Resolution: Implications For Atcase Mutants And The Mechanism Of Negative Cooperativity.
Proteins V. 15 147 1993
PubMed-ID: 8441751  |  Reference-DOI: 10.1002/PROT.340150206
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN
    Chains: A, C
    EC Number: 2.1.3.2
    Engineered: YES
    Gene: PYRB, B4245, JW4204
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ASPARTATE TRANSCARBAMYLASE, ATCASE
 
Molecule 2 - ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
    Chains: B, D
    Engineered: YES
    Gene: PYRI, B4244, JW4203
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CTP2Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CTP6Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:109 , CYS B:114 , CYS B:138 , CYS B:141BINDING SITE FOR RESIDUE ZN B 154
2AC2SOFTWARECYS D:109 , CYS D:114 , CYS D:138 , CYS D:141BINDING SITE FOR RESIDUE ZN D 154
3AC3SOFTWAREVAL B:9 , ALA B:11 , ILE B:12 , ASP B:19 , LYS B:60 , THR B:82 , ASN B:84 , TYR B:89 , VAL B:91 , LYS B:94BINDING SITE FOR RESIDUE CTP B 999
4AC4SOFTWAREGLU D:10 , ALA D:11 , ILE D:12 , LYS D:60 , THR D:82 , ASN D:84 , TYR D:89 , VAL D:91 , LYS D:94BINDING SITE FOR RESIDUE CTP D 999
5ZNBAUTHORCYS B:109 , CYS B:114 , CYS B:138 , CYS B:141ZN BINDING SITE OF CHAIN B
6ZNDAUTHORCYS D:109 , CYS D:114 , CYS D:138 , CYS D:141ZN BINDING SITE OF CHAIN D

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:267 -Pro A:268
2Leu C:267 -Pro C:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_ECOLI49-56
 		  2A:48-55
C:48-55
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_ECOLI49-56
 		  6A:48-55
C:48-55

(-) Exons   (0, 0)

(no "Exon" information available for 1RAA)

(-) 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:310
 aligned with PYRB_ECOLI | P0A786 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    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       311
           PYRB_ECOLI     2 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFETSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL 311
               SCOP domains d1raaa1 A:1-150 Aspartate carbamoyltransferase catalytic subunit                                                                                      d1raaa2 A:151-310 Aspartate carbamoyltransferase catalytic subunit                                                                                               SCOP domains
               CATH domains 1raaA01 A:1-133,A:292-310  [code=3.40.50.1370, no name defined]                                                                      1raaA02 A:134-291  [code=3.40.50.1370, no name defined]                                                                                                       1raaA01             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.......hhhhhhhhhhhhhhhh.........eeeeeee....hhhhhhhhhhhhhh.eeeeeee..............hhhhhhhhhhh.eeeeee....hhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh..eeeee..hhhhhh...eeeeeee....................hhhhhh.....eeee.........hhhhh.eee.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------CARBAMOY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1raa A   1 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFETSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL 310
                                    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       300       310


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with PYRI_ECOLI | P0A7F3 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
           PYRI_ECOLI     1 MTHDNKLQVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
               SCOP domains d1raab1 B:1-100 Aspartate carbamoyltransferase                                                      d1raab2 B:101-153                                     SCOP domains
               CATH domains -------1raaB01 B:8-100  [code=3.30.70.140, no name defined]                                         1raaB02 B:101-153  [code=2.30.30.20, no name defined] CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.....hhhhhhhhh.......eeeeee........eeeeeeee......hhhhhhhhh....eeeeee.....eeeee...eeee..................eeeeeee....eeeee....eeeehhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1raa B   1 MTHDNKLQVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   


Chain C from PDB  Type:PROTEIN  Length:310
 aligned with PYRB_ECOLI | P0A786 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    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       311
           PYRB_ECOLI     2 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFETSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL 311
               SCOP domains d1raac1 C:1-150 Aspartate carbamoyltransferase catalytic subunit                                                                                      d1raac2 C:151-310 Aspartate carbamoyltransferase catalytic subunit                                                                                               SCOP domains
               CATH domains 1raaC01 C:1-133,C:292-310  [code=3.40.50.1370, no name defined]                                                                      1raaC02 C:134-291  [code=3.40.50.1370, no name defined]                                                                                                       1raaC01             CATH domains
           Pfam domains (1) ------OTCace_N-1raaC03 C:7-148                                                                                                                      ----OTCace-1raaC01 C:153-303                                                                                                                               ------- Pfam domains (1)
           Pfam domains (2) ------OTCace_N-1raaC04 C:7-148                                                                                                                      ----OTCace-1raaC02 C:153-303                                                                                                                               ------- Pfam domains (2)
         Sec.struct. author ......eee.......hhhhhhhhhhhhhhhh.........eeeeeee....hhhhhhhhhhhhhh.eeeeeee..............hhhhhhhhhhh.eeeeee....hhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh..eeeee..hhhhhh...eeeeeee....................hhhhhh.....eeee.........hhhhh.eee.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------CARBAMOY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1raa C   1 ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFETSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL 310
                                    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       300       310


Chain D from PDB  Type:PROTEIN  Length:153
 aligned with PYRI_ECOLI | P0A7F3 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
           PYRI_ECOLI     1 MTHDNKLQVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
               SCOP domains d1raad1 D:1-100 Aspartate carbamoyltransferase                                                      d1raad2 D:101-153                                     SCOP domains
               CATH domains -------1raaD01 D:8-100  [code=3.30.70.140, no name defined]                                         1raaD02 D:101-153  [code=2.30.30.20, no name defined] CATH domains
           Pfam domains (1) ---PyrI-1raaD01 D:4-99                                                                             -PyrI_C-1raaD03 D:101-152                            - Pfam domains (1)
           Pfam domains (2) ---PyrI-1raaD02 D:4-99                                                                             -PyrI_C-1raaD04 D:101-152                            - Pfam domains (2)
         Sec.struct. author .............eeeeee.....hhhhhhhhh.......eeeeee........eeeeeeee......hhhhhhhhh....eeeeee.....eeeee...eeee..................eeeeeee....eeeee....eeeehhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1raa D   1 MTHDNKLQVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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  (3, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (3, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (4, 8)

Asymmetric Unit
(-)
Clan: no clan defined [family: OTCace] (48)
(-)
Clan: no clan defined [family: OTCace_N] (48)
(-)
Clan: no clan defined [family: PyrI] (22)
(-)
Clan: no clan defined [family: PyrI_C] (22)

(-) Gene Ontology  (16, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (PYRB_ECOLI | P0A786)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B,D   (PYRI_ECOLI | P0A7F3)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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: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.
cellular component
    GO:0009347    aspartate carbamoyltransferase complex    A multienzyme complex that catalyzes the formation N-carbamoyl-L-aspartate from carbamoyl phosphate and L-aspartate. It exhibits a variety of architectural organizations, but in all microorganisms the core catalytic component is a homotrimer of approximately 34 kDa polypeptides.
    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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  PYRB_ECOLI | P0A786
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  2.1.3.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRB_ECOLI | P0A786: 1acm 1at1 1d09 1ekx 1ezz 1f1b 1gq3 1i5o 1nbe 1q95 1r0b 1r0c 1rab 1rac 1rad 1rae 1raf 1rag 1rah 1rai 1sku 1tth 1tu0 1tug 1xjw 1za1 1za2 2a0f 2air 2at1 2atc 2fzc 2fzg 2fzk 2h3e 2hse 2ipo 2qg9 2qgf 3at1 3csu 3d7s 3mpu 3npm 4at1 4e2f 4f04 4fyv 4fyw 4fyx 4fyy 4wto 5at1 6at1 7at1 8at1 8atc 9atc
        PYRI_ECOLI | P0A7F3: 1acm 1at1 1d09 1ezz 1f1b 1i5o 1nbe 1q95 1r0b 1r0c 1rab 1rac 1rad 1rae 1raf 1rag 1rah 1rai 1sku 1tth 1tu0 1tug 1xjw 1za1 1za2 2a0f 2air 2at1 2atc 2fzc 2fzg 2fzk 2h3e 2hse 2ipo 2qg9 2qgf 3at1 3d7s 3mpu 4at1 4e2f 4f04 4fyv 4fyw 4fyx 4fyy 4wto 5at1 6at1 7at1 8at1 8atc 9atc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RAA)