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(-) Description

Title :  CARBAMATE KINASE FROM ENTEROCOCCUS FAECALIS BOUND TO MGADP
 
Authors :  S. Ramon-Maiques, A. Marina, V. Rubio
Date :  27 Mar 09  (Deposition) - 16 Mar 10  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.39
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Arginine Catabolism, Arginine Metabolism, Atp Synthesys, Kinase, Open Alpha/Beta Sheet, Phosphotransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ramon-Maiques, A. Marina, A. Guinot, F. Gil-Ortiz, M. Uriarte, I. Fita, V. Rubio
Substrate Binding And Catalysis In Carbamate Kinase Ascertained By Crystallographic And Site- Directed Mutagenesis Studies. Movements And Significance Of A Unique Globular Subdomain Of This Key Enzyme For Fermentative Atp Production In Bacteria.
J. Mol. Biol. V. 397 1261 2010
PubMed-ID: 20188742  |  Reference-DOI: 10.1016/J.JMB.2010.02.038
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBAMATE KINASE 1
    Chains: A, B, C
    EC Number: 2.7.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Synonym: CARBAMATE KINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , GLY A:11 , LYS A:209 , THR A:229 , GLY A:230 , CYS A:235 , TYR A:238 , HIS A:262 , PHE A:263 , ALA A:264 , SER A:267 , MET A:268 , LYS A:271 , MG A:1312 , HOH A:2255 , HOH A:2257 , HOH A:2298 , HOH A:2299 , HOH A:2300 , HOH A:2301 , HOH A:2302 , HOH A:2303 , HOH A:2304 , HOH A:2305 , HOH A:2306 , HOH A:2307 , HOH A:2308BINDING SITE FOR RESIDUE ADP A1311
2AC2SOFTWAREADP A:1311 , HOH A:2255 , HOH A:2257 , HOH A:2306 , HOH A:2308BINDING SITE FOR RESIDUE MG A1312
3AC3SOFTWAREHOH A:2306 , HOH A:2307 , HOH A:2308 , HOH A:2309 , HOH A:2310BINDING SITE FOR RESIDUE ACT A1313
4AC4SOFTWAREHOH A:2235 , HOH A:2296 , GLY B:10 , GLY B:11 , LYS B:209 , THR B:229 , GLY B:230 , VAL B:231 , CYS B:235 , TYR B:238 , HIS B:262 , ALA B:264 , SER B:267 , MET B:268 , LYS B:271 , MG B:1312 , HOH B:2250 , HOH B:2252 , HOH B:2273 , HOH B:2274 , HOH B:2275 , HOH B:2276 , HOH B:2277 , HOH B:2278 , HOH B:2279 , HOH B:2280 , HOH B:2282BINDING SITE FOR RESIDUE ADP B1311
5AC5SOFTWAREADP B:1311 , HOH B:2250 , HOH B:2252 , HOH B:2277 , HOH B:2282BINDING SITE FOR RESIDUE MG B1312
6AC6SOFTWAREGLY C:10 , GLY C:11 , LYS C:209 , THR C:229 , GLY C:230 , VAL C:231 , CYS C:235 , TYR C:238 , HIS C:262 , PHE C:263 , ALA C:264 , SER C:267 , MET C:268 , LYS C:271 , MG C:1312 , HOH C:2210 , HOH C:2213 , HOH C:2239 , HOH C:2240 , HOH C:2241 , HOH C:2242 , HOH C:2243 , HOH C:2244 , HOH C:2246 , HOH C:2247BINDING SITE FOR RESIDUE ADP C1311
7AC7SOFTWAREADP C:1311 , HOH C:2210 , HOH C:2213 , HOH C:2241 , HOH C:2246BINDING SITE FOR RESIDUE MG C1312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WE5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WE5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WE5)

(-) Exons   (0, 0)

(no "Exon" information available for 2WE5)

(-) 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:309
 aligned with ARCC1_ENTFA | P0A2X7 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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         
          ARCC1_ENTFA     2 GKKMVVALGGNAILSNDASAHAQQQALVQTSAYLVHLIKQGHRLIVSHGNGPQVGNLLLQQQAADSEKNPAMPLDTCVAMTQGSIGYWLSNALNQELNKAGIKKQVATVLTQVVVDPADEAFKNPTKPIGPFLTEAEAKEAMQAGAIFKEDAGRGWRKVVPSPKPIDIHEAETINTLIKNDIITISCGGGGIPVVGQELKGVEAVIDKDFASEKLAELVDADALVILTGVDYVCINYGKPDEKQLTNVTVAELEEYKQAGHFAPGSMLPKIEAAIQFVESQPNKQAIITSLENLGSMSGDEIVGTVVTK 310
               SCOP domains d2we5a_ A: Carbamate kinase                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2we5A00 A:2-310  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eeee...hhhhhh..eeeeeeehhhhhhhhhh....eee.....eeeee....eeee.hhhhhhhhhhh..eee.hhhhheeee....ee.....hhhhhhhhhhhhh...eeeee......ee.......ee..eeehhhhhhhhhh.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2we5 A   2 GKKMVVALGGNAILSNDASAHAQQQALVQTSAYLVHLIKQGHRLIVSHGNGPQVGNLLLQQQAADSEKNPAMPLDTCVAMTQGSIGYWLSNALNQELNKAGIKKQVATVLTQVVVDPADEAFKNPTKPIGPFLTEAEAKEAMQAGAIFKEDAGRGWRKVVPSPKPIDIHEAETINTLIKNDIITISCGGGGIPVVGQELKGVEAVIDKDFASEKLAELVDADALVILTGVDYVCINYGKPDEKQLTNVTVAELEEYKQAGHFAPGSMLPKIEAAIQFVESQPNKQAIITSLENLGSMSGDEIVGTVVTK 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         


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with ARCC1_ENTFA | P0A2X7 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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         
          ARCC1_ENTFA     2 GKKMVVALGGNAILSNDASAHAQQQALVQTSAYLVHLIKQGHRLIVSHGNGPQVGNLLLQQQAADSEKNPAMPLDTCVAMTQGSIGYWLSNALNQELNKAGIKKQVATVLTQVVVDPADEAFKNPTKPIGPFLTEAEAKEAMQAGAIFKEDAGRGWRKVVPSPKPIDIHEAETINTLIKNDIITISCGGGGIPVVGQELKGVEAVIDKDFASEKLAELVDADALVILTGVDYVCINYGKPDEKQLTNVTVAELEEYKQAGHFAPGSMLPKIEAAIQFVESQPNKQAIITSLENLGSMSGDEIVGTVVTK 310
               SCOP domains d2we5b_ B: Carbamate kinase                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2we5B00 B:2-310  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eeee...hhhhh...eeeeeeehhhhhhhhh.....eeee...eeeeee....eeee.hhhhhhhhhhh..eee.hhhhheeee....ee.....hhhhhhhhhhhhh...eeeee......ee.......ee..eeehhhhhhhhhh.......hhhhhhhhhhhhhhh...eeeee.hhhhhhh.......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2we5 B   2 GKKMVVALGGNAILSNDASAHAQQQALVQTSAYLVHLIKQGHRLIVSHGNGPQVGNLLLQQQAADSEKNPAMPLDTCVAMTQGSIGYWLSNALNQELNKAGIKKQVATVLTQVVVDPADEAFKNPTKPIGPFLTEAEAKEAMQAGAIFKEDAGRGWRKVVPSPKPIDIHEAETINTLIKNDIITISCGGGGIPVVGQELKGVEAVIDKDFASEKLAELVDADALVILTGVDYVCINYGKPDEKQLTNVTVAELEEYKQAGHFAPGSMLPKIEAAIQFVESQPNKQAIITSLENLGSMSGDEIVGTVVTK 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         


Chain C from PDB  Type:PROTEIN  Length:309
 aligned with ARCC1_ENTFA | P0A2X7 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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         
          ARCC1_ENTFA     2 GKKMVVALGGNAILSNDASAHAQQQALVQTSAYLVHLIKQGHRLIVSHGNGPQVGNLLLQQQAADSEKNPAMPLDTCVAMTQGSIGYWLSNALNQELNKAGIKKQVATVLTQVVVDPADEAFKNPTKPIGPFLTEAEAKEAMQAGAIFKEDAGRGWRKVVPSPKPIDIHEAETINTLIKNDIITISCGGGGIPVVGQELKGVEAVIDKDFASEKLAELVDADALVILTGVDYVCINYGKPDEKQLTNVTVAELEEYKQAGHFAPGSMLPKIEAAIQFVESQPNKQAIITSLENLGSMSGDEIVGTVVTK 310
               SCOP domains d2we5c_ C: Carbamate kinase                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2we5C00 C:2-310  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) -AA_kinase-2we5C01 C:3-291                                                                                                                                                                                                                                                                        ------------------- Pfam domains (1)
           Pfam domains (2) -AA_kinase-2we5C02 C:3-291                                                                                                                                                                                                                                                                        ------------------- Pfam domains (2)
           Pfam domains (3) -AA_kinase-2we5C03 C:3-291                                                                                                                                                                                                                                                                        ------------------- Pfam domains (3)
         Sec.struct. author ..eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eeee...hhhhh...eeeeeeehhhhhhhhhhhh..eee.....eeeee....eeee.hhhhhhhhhh...eee.hhhhheeee....ee.....hhhhhhhhhhhhh...eeeee......ee.......ee..eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeee.hhhhhhh.......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2we5 C   2 GKKMVVALGGNAILSNDASAHAQQQALVQTSAYLVHLIKQGHRLIVSHGNGPQVGNLLLQQQAADSEKNPAMPLDTCVAMTQGSIGYWLSNALNQELNKAGIKKQVATVLTQVVVDPADEAFKNPTKPIGPFLTEAEAKEAMQAGAIFKEDAGRGWRKVVPSPKPIDIHEAETINTLIKNDIITISCGGGGIPVVGQELKGVEAVIDKDFASEKLAELVDADALVILTGVDYVCINYGKPDEKQLTNVTVAELEEYKQAGHFAPGSMLPKIEAAIQFVESQPNKQAIITSLENLGSMSGDEIVGTVVTK 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
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: AA_kinase] (20)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (ARCC1_ENTFA | P0A2X7)
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:0035975    carbamoyl phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbamoyl phosphate, an intermediate in the urea cycle and other nitrogen compound metabolic pathways.
    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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        ARCC1_ENTFA | P0A2X7: 2we4

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