ATCase Complex with CTP (5AT1)

by Natalia Lukina
 

General Information SCOP Classification CATH Classification Comparing Sequences vs. Comparing Structures References

General Information

5AT1 is a complex of Aspartate Carbamoyltransferase (Aspartate Transcarbamylase/ATCase) in T-state (T is an abbreviation for tense and is used to indicate the conformational state of the enzyme that has unit cell dimensions of u = 122 A and c = 142 A in the space group P321) from Escherichia coli (E.C. 2.1.3.2) with Cytidine 5-Prime-Triphosphate (CTP).

The feedback of ATCase regulates pyrimidine synthesis, it catalyzes the formation of N-carbamoyl aspartate from carbamoyl phosphate and aspartate. Moreover, ATCase is allosterically inhibited by CTP, a pyrimidine nucleotide, and is allosterically activated by ATP, a purine nucleotide. Its basically a regulator of enzyme activity. It catalyzes condensation of carbamoyl phosphate with aspartate to form carbamoyl aspartate.

ATCase is susceptible to feedback regulation and is inhibited by cytidine 5’-triphosphate (CTP), a product of the pyrimidine pathway. Conversely, a product of the parallel purine pathway, adenosine 5’-triphosphate (ATP), stimulates the enzymatic activity (see structure 7AT1). ATCase is a hexamer in both catalytic and regulatory chains, e.g. it is composed of six catalytic chains and six regulatory chains that can be dissociated into subunits. The asymmetric unit of the crystal consists of one third of the molecule - two catalytic and two regulatory chains: chains A and C are the catalytic chains consisting of 310 residues each. Chains B and D are the regulatory chains consisting of 153 residues each.

Experimental Method: X-ray Diffraction
Classification: Transferase (Carbamoyl-P, Aspartate)
EC Number: 2.1.3.2
Source: Escherichia coli

Resolution:  2.60 A
R-value:  0.160
Space Group: P 3 2 1
Unit Cell Dimensions [Å]: a 122.00 b 122.00 c 142.00
angles [°]: alpha 90.00 beta 90.00 gamma 120.00

Polymer Chains: A, B, C, D
Residues: 926
Atoms: 7166
 

Figure1. 5AT1 structure generated by RasMol. Displayed using ribbons model, colored by groups.

Figure2. 5AT1 structure generated by RasMol. Displayed using balls and sticks model, colored by chains.

SCOP Classification

Protein: Aspartate carbamoyltransferase catalytic subunit from Escherichia coli
Lineage:

1. Root: scop
2. Class: Alpha and beta proteins (a/b)
   Mainly parallel beta sheets (beta-alpha-beta units)
3. Fold: ATC-like
   consists of two similar domains related by pseudodyad; duplication
   core: 3 layers, a/b/a, parallel beta-sheet of 4 strands, order 2134
4. Superfamily: Aspartate/ornithine carbamoyltransferase
5. Family: Aspartate/ornithine carbamoyltransferase
6. Protein: Aspartate carbamoyltransferase catalytic subunit
7. Species: Escherichia coli

28 PDB Entry Domains

Protein: Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain from Escherichia coli
Lineage:

1. Root: scop
2. Class: Small proteins
   Usually dominated by metal ligand, heme, and/or disulfide bridges
3. Fold: Rubredoxin-like
   metal(zinc or iron)-bound fold; sequence contains two CX(n)C motifs, in most cases n = 2
4. Superfamily: Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
5. Family: Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
6. Protein: Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
7. Species: Escherichia coli

26 PDB Entry Domains

CATH - Protein Structure Classification

5AT1A - 3 related domains

5AT1B - 3 related domains

5AT1C - 3 related domains

5AT1D - 3 related domains

Secondary Structure
www.biochem.ucl.ac.uk/bsm/pdbsum/5at1/main.html

Comparing Sequences vs. Comparing Structures

Chose 5AT1A (length - 310) for structure comparison
Parameters: Z-Score>4.5 RMSD<3.0Å Sequence identity<30.0%
Results of sequence comparison based on structure alignment:
 

5AT1:A    3/4     PLYQKHIISINDLSRDDLNLVLATAAKLKANP-----QPELLKHKVIASCFFEASTRTRL
1C9Y:A    3/37    QLKGRDLLTLKNFTGEEIKYMLWLSADLKFRIKQKGEYLPLLQGKSLGMIFEKRSTRTRL
1ORT:A    3/4     NMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGT-EQQHLKRKNIALIFEKTSTRTRC

5AT1:A   58/59    SFQTSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATE
1C9Y:A   63/97    STETGFALLGGHPCFL-TTQDIHLGV-NESLTDTARVLSSMADAVLARVYKQSDLDTLAK
1ORT:A   62/63    AFEVAAYDQGANVTYIDP-NSSQIG-HKESMKDTARVLGRMYDAIGYRGFKQEIVEELAK

5AT1:A  118/119   FSGNVPVLNAGDGSNQHPTQTLLDLFTIQQTE-GRLDNLHVAMVGDLKYGRTVHSLTQAL
1C9Y:A  121/155   EAS-IPIINGLS-DLYHPIQILADYLTLQEHY-SSLKGLTLSWIGDG--NNILHSIMMSA
1ORT:A  120/121   FAG-VPVFNGLTD-EYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNN-MGNSLLLIG

5AT1:A  177/178   AKFDGNRFYFIAPDALAMPEYILDMLDEKG----IAWSLHSSIEEVMAEVDILYMTR---
1C9Y:A  176/210   AKFG-MHLQAATPKGYEPDASVTKLAEQYAKENGTKLLLTNDPLEAAHGGNVLITDTWIS
1ORT:A  177/178   AKLG-MDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVS

5AT1:A  230/231   ---------------VQKERLDPSEYANVKAQFVLRASDLHNA-KANMKVLHPLPRV---
1C9Y:A  235/269   MGREEEKKKRLQAF-Q---------------GYQVTMKTAKVA-ASDWTFLHCLPRKP--
1ORT:A  236/237   MGEPVEAWGERIKELL---------------PYQVNMEIMKATGNPRAKFMHCLPAFHNS

5AT1:A  271/272   ------------------DEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL
1C9Y:A  276/310   ------------------EEVDDEVFYSPRSLVFPEAENRKWTIMAVMVSLLTDYSPQ
1ORT:A  281/282   ETKVGKQIAEQYPNLANGIEVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI---

Results based on sequence comparison (from ClustalW)

References

1. Stevens RC, Gouaux JE, Lipscomb WN. Structural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6-A resolution. Biochemistry 1990 Aug 21;29(33):7691-701 [pdf]
2. www.pdb.org
3. www.biochem.ucl.ac.uk/bsm/cath_new/index.html
4. scop.berkeley.edu
5. www.ebi.ac.uk/clustalw
6. www.biochem.ucl.ac.uk/bsm/pdbsum/5at1/main.html