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(-) Description

Title :  THE R STATE STRUCTURE OF E. COLI ATCASE WITH UTP AND MAGNESIUM BOUND
 
Authors :  G. M. Cockrell, Y. Zheng, W. Guo, A. W. Peterson, E. R. Kantrowitz
Date :  29 Apr 13  (Deposition) - 27 Nov 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Pyrimidine Nucleotide Biosynthesis, Feedback Inhibition, Competing Pathway Product Activation, Allostery, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. M. Cockrell, Y. Zheng, W. Guo, A. W. Peterson, J. K. Truong, E. R. Kantrowitz
New Paradigm For Allosteric Regulation Of Escherichia Coli Aspartate Transcarbamoylase.
Biochemistry V. 52 8036 2013
PubMed-ID: 24138583  |  Reference-DOI: 10.1021/BI401205N

(-) Compounds

Molecule 1 - ASPARTATE CARBAMOYLTRANSFERASE
    Chains: A, C
    EC Number: 2.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYRB, EKO11_4066, KO11_22860
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 595495
    Strain: ATCC 55124 / KO11
    Synonym: ASPARTATE TRANSCARBAMYLASE
 
Molecule 2 - ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
    Chains: B, D
    EC Number: 2.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYRI, EKO11_4067, KO11_22855
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 595495
    Strain: ATCC 55124 / KO11

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PAL2Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID
3UTP4Ligand/IonURIDINE 5'-TRIPHOSPHATE
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PAL6Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID
3UTP12Ligand/IonURIDINE 5'-TRIPHOSPHATE
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:52 , THR A:53 , ARG A:54 , THR A:55 , SER A:80 , LYS A:84 , ARG A:105 , HIS A:134 , ARG A:167 , ARG A:229 , GLN A:231 , LEU A:267 , HOH A:506 , HOH A:538BINDING SITE FOR RESIDUE PAL A 401
02AC2SOFTWARECYS B:109 , CYS B:114 , CYS B:138 , CYS B:141BINDING SITE FOR RESIDUE ZN B 201
03AC3SOFTWAREALA B:11 , ILE B:12 , VAL B:17 , HIS B:20 , LYS B:60 , TYR B:89 , LYS B:94 , UTP B:203 , MG B:204 , HOH B:301 , HOH B:302BINDING SITE FOR RESIDUE UTP B 202
04AC4SOFTWAREGLU B:10 , HIS B:20 , LEU B:48 , PRO B:49 , SER B:50 , GLU B:52 , LYS B:56 , LYS B:60 , UTP B:202 , MG B:204 , HOH B:301 , HOH B:302 , ARG D:41BINDING SITE FOR RESIDUE UTP B 203
05AC5SOFTWAREUTP B:202 , UTP B:203 , HOH B:301 , HOH B:302BINDING SITE FOR RESIDUE MG B 204
06AC6SOFTWARESER C:52 , THR C:53 , ARG C:54 , THR C:55 , SER C:80 , LYS C:84 , ARG C:105 , HIS C:134 , ARG C:167 , THR C:168 , ARG C:229 , GLN C:231 , LEU C:267 , HOH C:509 , HOH C:528 , HOH C:531BINDING SITE FOR RESIDUE PAL C 401
07AC7SOFTWARECYS D:109 , CYS D:114 , CYS D:138 , CYS D:141BINDING SITE FOR RESIDUE ZN D 201
08AC8SOFTWAREALA D:11 , ILE D:12 , HIS D:20 , LYS D:60 , TYR D:89 , LYS D:94 , UTP D:203 , MG D:204 , HOH D:301 , HOH D:302 , HOH D:318BINDING SITE FOR RESIDUE UTP D 202
09AC9SOFTWAREARG B:41 , HIS D:20 , LEU D:48 , PRO D:49 , SER D:50 , GLY D:51 , GLU D:52 , LYS D:56 , LEU D:58 , LYS D:60 , UTP D:202 , MG D:204 , HOH D:301 , HOH D:302BINDING SITE FOR RESIDUE UTP D 203
10BC1SOFTWAREUTP D:202 , UTP D:203 , HOH D:301 , HOH D:302BINDING SITE FOR RESIDUE MG D 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KGZ)

(-) 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 4KGZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KGZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4KGZ)

(-) 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
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4kgza1 A:1-150 Aspartate carbamoyltransferase catalytic subunit                                                                                      d4kgza2 A:151-310 Aspartate carbamoyltransferase catalytic subunit                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhh..hhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee....hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh.....eeeee.hhhhh.hhhhhhhhhhh..eeee..hhhhhhh...eeee........hhhhhhhh......hhhhhh......eee.........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgz 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:144
                                                                                                                                                                                
               SCOP domains d4kgzb1 B:10-100 Aspartate carbamoyltransferase                                            d4kgzb2 B:101-153                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhh........eeeeeeee.....eeeeeeee....hhhhhhhhhhh....eeeeee..eeeeee......eee...................eeeeeee..eeeeee.....eee.hhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kgz B  10 EAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149    


Chain C from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4kgzc1 C:1-150 Aspartate carbamoyltransferase catalytic subunit                                                                                      d4kgzc2 C:151-310 Aspartate carbamoyltransferase catalytic subunit                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhh..hhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee....hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh.....eeeee.hhhhh.hhhhhhhhhhh...eee............eeee...hhhhhhhhhhhhh......hhhhhh......eee.........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgz 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:143
                                                                                                                                                                               
               SCOP domains d4kgzd1 D:11-100 Aspartate carbamoyltransferase                                           d4kgzd2 D:101-153                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..hhhhhhhhh........eeeeeeeee...eeeeeeeee....hhhhhhhhhhhh...eeeeee..eeeeee......eee.........hhhhh.....eeeee......eeee.....eeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgz D  11 AIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
                                    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  (0, 0)

(no "CATH Domain" information available for 4KGZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KGZ)

(-) Gene Ontology  (12, 15)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4kgv 4kgx 4kh0 4kh1