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(-) Description

Title :  CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES
 
Authors :  T. Nakai, T. Hasegawa, E. Yamashita, M. Yamamoto, T. Kumasaka, T. Ueki, Y. Ikenaka, S. Takahashi, M. Sato, T. Tsukihara
Date :  06 Apr 00  (Deposition) - 06 Apr 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Four-Layer Sandwich, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nakai, T. Hasegawa, E. Yamashita, M. Yamamoto, T. Kumasaka, T. Ueki H. Nanba, Y. Ikenaka, S. Takahashi, M. Sato, T. Tsukihara
Crystal Structure Of N-Carbamyl-D-Amino Acid Amidohydrolase With A Novel Catalytic Framework Common To Amidohydrolases.
Structure Fold. Des. V. 8 729 2000
PubMed-ID: 10903946  |  Reference-DOI: 10.1016/S0969-2126(00)00160-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE
    Chains: A, B
    EC Number: 3.5.1.77
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAD108
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AGROBACTERIUM SP.
    Organism Taxid: 252128
    Strain: KNK712

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ERZ)

(-) Sites  (0, 0)

(no "Site" information available for 1ERZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Met A:72 -Pro A:73
2Met B:72 -Pro B:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CN_HYDROLASEPS50263 Carbon-nitrogen hydrolase domain profile.DCAS_AGRSK5-276
 		  2A:4-275
B:4-275
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CN_HYDROLASEPS50263 Carbon-nitrogen hydrolase domain profile.DCAS_AGRSK5-276
 		  4A:4-275
B:4-275

(-) Exons   (0, 0)

(no "Exon" information available for 1ERZ)

(-) 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:303
 aligned with DCAS_AGRSK | P60327 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:303
                                    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   
           DCAS_AGRSK     2 TRQMILAVGQQGPIARAETREQVVVRLLDMLTKAASRGANFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFEKAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPEAWRVMGLRGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEENCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKQHRQPQHYGLIAEL 304
               SCOP domains d1erza_ A: N-carbamoyl-D-aminoacid amidohydrolase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1erzA00 A:1-303  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee........hhhhhhhhhhhhhhhhhhh...eee........hhhhh...hhhhhhh..........hhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeee.....eeeeee..................hhhhhh........eeee..eeeee.hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..eee..eee....eee.....eeee......eeeeeeee...hhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---CN_HYDROLASE  PDB: A:4-275 UniProt: 5-276                                                                                                                                                                                                                                       ---------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1erz A   1 TRQMILAVGQQGPIARAETREQVVVRLLDMLTKAASRGANFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFEKAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPEAWRVMGLRGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEENCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKQHRQPQHYGLIAEL 303
                                    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   


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with DCAS_AGRSK | P60327 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:303
                                    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   
           DCAS_AGRSK     2 TRQMILAVGQQGPIARAETREQVVVRLLDMLTKAASRGANFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFEKAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPEAWRVMGLRGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEENCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKQHRQPQHYGLIAEL 304
               SCOP domains d1erzb_ B: N-carbamoyl-D-aminoacid amidohydrolase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1erzB00 B:1-303  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee........hhhhhhhhhhhhhhhhhhh...eee........hhhhh...hhhhhhh..........hhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeee.....eeeeee..................hhhhhh........eeee..eeeee.hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..eee..eee....eee.....eeee......eeeeeeee...hhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---CN_HYDROLASE  PDB: B:4-275 UniProt: 5-276                                                                                                                                                                                                                                       ---------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1erz B   1 TRQMILAVGQQGPIARAETREQVVVRLLDMLTKAASRGANFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFEKAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPEAWRVMGLRGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEENCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKQHRQPQHYGLIAEL 303
                                    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
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DCAS_AGRSK | P60327)
molecular function
    GO:0047417    N-carbamoyl-D-amino acid hydrolase activity    Catalysis of the reaction: H2O + N-carbamoyl-D-amino acid = CO2 + NH3 + D-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
biological process
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

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  Cis Peptide Bonds
    Met A:72 - Pro A:73   [ RasMol ]  
    Met B:72 - Pro B:73   [ RasMol ]  
 
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 Related Entries

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UniProtKB/Swiss-Prot
        DCAS_AGRSK | P60327: 1uf4 1uf5 1uf7 1uf8

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