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(-) Description

Title :  STRUCTURE OF THE CARBAMATE KINASE-LIKE CARBAMOYL PHOSPHATE SYNTHETASE FROM THE HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS FURIOSUS BOUND TO ADP
 
Authors :  S. Ramon-Maiques, A. Marina, M. Uriarte, I. Fita, V. Rubio
Date :  28 Apr 00  (Deposition) - 04 Jul 00  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Hyperthermophiles, Adp Site, Arginine Metabolism Phosphoryl Group Transfer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ramon-Maiques, A. Marina, M. Uriarte, I. Fita, V. Rubio
The 1. 5-A Resolution Crystal Structure Of The Carbamate Kinase-Like Carbamoyl Phosphate Synthetase From The Hyperthermophilic Archaeon Pyrococcus Furiosus, Bound To Adp, Confirms That This Thermoestable Enzyme Is A Carbamate Kinase, And Provides Insights Into Substrate Binding And Stability In Carbamate Kinases
J. Mol. Biol. V. 299 463 2000
PubMed-ID: 10860751  |  Reference-DOI: 10.1006/JMBI.2000.3779

(-) Compounds

Molecule 1 - CARBAMATE KINASE
    Chains: A, B
    EC Number: 2.7.2.2
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: CARBAMATE KINASE-LIKE CARBAMOYLPHOSPHATE SYNTETASE, CARBAMATE KINASE-LIKE CARBAMOYLPHOSPHATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREADP A:315 , HOH A:2342 , HOH A:2344 , HOH A:2389 , HOH A:2391BINDING SITE FOR RESIDUE MG A 316
2AC2SOFTWAREADP B:315 , HOH B:2286 , HOH B:2288 , HOH B:2320 , HOH B:2323BINDING SITE FOR RESIDUE MG B 316
3AC3SOFTWAREGLY A:10 , GLY A:11 , LYS A:215 , THR A:235 , ASP A:236 , VAL A:237 , ALA A:241 , TYR A:244 , HIS A:268 , PHE A:269 , LYS A:270 , SER A:273 , MET A:274 , LYS A:277 , MG A:316 , HOH A:2380 , HOH A:2381 , HOH A:2382 , HOH A:2383 , HOH A:2384 , HOH A:2385 , HOH A:2386 , HOH A:2388 , HOH A:2390BINDING SITE FOR RESIDUE ADP A 315
4AC4SOFTWAREGLY B:10 , GLY B:11 , LYS B:215 , THR B:235 , ASP B:236 , GLY B:239 , ALA B:241 , TYR B:244 , HIS B:268 , PHE B:269 , LYS B:270 , SER B:273 , MET B:274 , LYS B:277 , MG B:316 , HOH B:2248 , HOH B:2315 , HOH B:2316 , HOH B:2317 , HOH B:2318 , HOH B:2319 , HOH B:2320 , HOH B:2321 , HOH B:2322 , HOH B:2324 , HOH B:2325BINDING SITE FOR RESIDUE ADP B 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E19)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E19)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E19)

(-) Exons   (0, 0)

(no "Exon" information available for 1E19)

(-) 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:313
 aligned with CPKA_PYRFU | P95474 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:313
                                    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   
           CPKA_PYRFU     2 GKRVVIALGGNALQQRGQKGSYEEMMDNVRKTARQIAEIIARGYEVVITHGNGPQVGSLLLHMDAGQATYGIPAQPMDVAGAMSQGWIGYMIQQALKNELRKRGMEKKVVTIITQTIVDKNDPAFQNPTKPVGPFYDEETAKRLAREKGWIVKEDSGRGWRRVVPSPDPKGHVEAETIKKLVERGVIVIASGGGGVPVILEDGEIKGVEAVIDKDLAGEKLAEEVNADIFMILTDVNGAALYYGTEKEQWLREVKVEELRKYYEEGHFKAGSMGPKVLAAIRFIEWGGERAIIAHLEKAVEALEGKTGTQVLP 314
               SCOP domains d1e19a_ A: Carbamate kinase                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1e19A00 A:2-314  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eeee...hhhhh...eee....hhhhhhhhhhhhh.eeee.....eeeee....eeee.hhhhhhhhhhh..eee.hhhhheeeeee..eeee.....hhhhhhhhhhhhh...eeeeee..................eeehhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeee..hhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e19 A   2 GKRVVIALGGNALQQRGQKGSYEEMMDNVRKTARQIAEIIARGYEVVITHGNGPQVGSLLLHMDAGQATYGIPAQPMDVAGAMSQGWIGYMIQQALKNELRKRGMEKKVVTIITQTIVDKNDPAFQNPTKPVGPFYDEETAKRLAREKGWIVKEDSGRGWRRVVPSPDPKGHVEAETIKKLVERGVIVIASGGGGVPVILEDGEIKGVEAVIDKDLAGEKLAEEVNADIFMILTDVNGAALYYGTEKEQWLREVKVEELRKYYEEGHFKAGSMGPKVLAAIRFIEWGGERAIIAHLEKAVEALEGKTGTQVLP 314
                                    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   


Chain B from PDB  Type:PROTEIN  Length:313
 aligned with CPKA_PYRFU | P95474 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:313
                                    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   
           CPKA_PYRFU     2 GKRVVIALGGNALQQRGQKGSYEEMMDNVRKTARQIAEIIARGYEVVITHGNGPQVGSLLLHMDAGQATYGIPAQPMDVAGAMSQGWIGYMIQQALKNELRKRGMEKKVVTIITQTIVDKNDPAFQNPTKPVGPFYDEETAKRLAREKGWIVKEDSGRGWRRVVPSPDPKGHVEAETIKKLVERGVIVIASGGGGVPVILEDGEIKGVEAVIDKDLAGEKLAEEVNADIFMILTDVNGAALYYGTEKEQWLREVKVEELRKYYEEGHFKAGSMGPKVLAAIRFIEWGGERAIIAHLEKAVEALEGKTGTQVLP 314
               SCOP domains d1e19b_ B: Carbamate kinase                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1e19B00 B:2-314  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eee....hhhhhh..eee....hhhhhhhhhhhhh.eeee.....eeeee.........hhhhhhhhhhh..eee.hhhhheeeeee..eeee.....hhhhhhhhhhhhh...eeeeee..................eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e19 B   2 GKRVVIALGGNALQQRGQKGSYEEMMDNVRKTARQIAEIIARGYEVVITHGNGPQVGSLLLHMDAGQATYGIPAQPMDVAGAMSQGWIGYMIQQALKNELRKRGMEKKVVTIITQTIVDKNDPAFQNPTKPVGPFYDEETAKRLAREKGWIVKEDSGRGWRRVVPSPDPKGHVEAETIKKLVERGVIVIASGGGGVPVILEDGEIKGVEAVIDKDLAGEKLAEEVNADIFMILTDVNGAALYYGTEKEQWLREVKVEELRKYYEEGHFKAGSMGPKVLAAIRFIEWGGERAIIAHLEKAVEALEGKTGTQVLP 314
                                    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
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E19)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CPKA_PYRFU | P95474)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008804    carbamate kinase activity    Catalysis of the reaction: ATP + NH3 + CO2 = ADP + carbamoyl phosphate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
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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 Related Entries

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(-) Related Entries Specified in the PDB File

1b7b CARBAMATE KINASE FROM ENTEROCOCCUS FAECIUM