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(-) Description

Title :  THE R STATE STRUCTURE OF E. COLI ATCASE WITH ATP 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 :  2.25
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
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3PAL2Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1ATP12Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PAL6Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID
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:514 , HOH A:515 , HOH A:517BINDING 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 , ASP B:19 , HIS B:20 , LYS B:60 , ASN B:84 , ILE B:86 , TYR B:89 , VAL B:91 , LYS B:94 , ATP B:203 , MG B:204 , HOH B:302 , HOH B:358 , HOH B:359 , LYS D:6BINDING SITE FOR RESIDUE ATP B 202
04AC4SOFTWAREHIS B:20 , THR B:43 , LEU B:48 , PRO B:49 , SER B:50 , GLY B:51 , GLU B:52 , LYS B:56 , LYS B:60 , ATP B:202 , MG B:204 , HOH B:301 , HOH B:302 , HOH B:358 , LYS D:6 , VAL D:9 , THR D:43BINDING SITE FOR RESIDUE ATP B 203
05AC5SOFTWAREATP B:202 , ATP B:203 , HOH B:302 , LYS D:6BINDING 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:506 , HOH C:540 , HOH C:617BINDING SITE FOR RESIDUE PAL C 401
07AC7SOFTWARECYS D:109 , CYS D:114 , CYS D:138 , CYS D:141BINDING SITE FOR RESIDUE ZN D 201
08AC8SOFTWARELYS B:6 , LEU B:7 , ALA D:11 , ILE D:12 , VAL D:17 , ASP D:19 , HIS D:20 , LYS D:60 , ILE D:86 , TYR D:89 , LYS D:94 , ATP D:203 , MG D:204 , HOH D:301 , HOH D:302 , HOH D:309 , HOH D:336BINDING SITE FOR RESIDUE ATP D 202
09AC9SOFTWARELYS B:6 , VAL B:9 , GLU B:10 , HIS D:20 , LEU D:48 , PRO D:49 , SER D:50 , GLY D:51 , GLU D:52 , LYS D:56 , LYS D:60 , ATP D:202 , MG D:204 , HOH D:301 , HOH D:302 , HOH D:336BINDING SITE FOR RESIDUE ATP D 203
10BC1SOFTWAREATP D:202 , ATP D:203 , HOH D:301 , HOH D:302BINDING SITE FOR RESIDUE MG D 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KH0)

(-) 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 4KH0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KH0)

(-) Exons   (0, 0)

(no "Exon" information available for 4KH0)

(-) 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 d4kh0a1 A:1-150 Aspartate carbamoyltransferase catalytic subunit                                                                                      d4kh0a2 A:151-310 Aspartate carbamoyltransferase catalytic subunit                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh.hhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee....hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh.....eeeee.hhhhh.hhhhhhhhhhh...eee...hhhhhh...eeee........hhhhhhhh......hhhhhh......eee.........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kh0 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:150
                                                                                                                                                                                      
               SCOP domains d4kh0b1 B:4-100 Aspartate carbamoyltransferase                                                   d4kh0b2 B:101-153                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeee..hhhhhhhhh........eeeeeeeee...eeeeeeeee....hhhhhhhhhhh....eeeeee..eeeeee......eee.........hhhhh.....eeeeeee..eeeeee.....eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kh0 B   4 DNKLQVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153


Chain C from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4kh0c1 C:1-150 Aspartate carbamoyltransferase catalytic subunit                                                                                      d4kh0c2 C:151-310 Aspartate carbamoyltransferase catalytic subunit                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh..eeeee.....hhhhhh..hhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee....hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh.....eeeee.hhhhh.hhhhhhhhhh....eee...hhhhhh...eeee........hhhhhhhh......hhhhhh......eee.........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kh0 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:152
                                                                                                                                                                                        
               SCOP domains d4kh0d1 D:2-100 Aspartate carbamoyltransferase                                                     d4kh0d2 D:101-153                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee...hhhhhhhhh........eeeeeeeee...eeeeeeeee....hhhhhhhhhhhh...eeeeee..eeeeee......eee.........hhhhh.....eeeeee....eeeee.....eeehhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kh0 D   2 THDNKLQVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4KH0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KH0)

(-) Gene Ontology  (12, 15)

Asymmetric Unit(hide GO term definitions)

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  2.1.3.2
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 Related Entries

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(-) Related Entries Specified in the PDB File

4kgv 4kgx 4kgz 4kh1