Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  THE MUTANT A302C OF AGROBACTERIUM RADIOBACTER N-CARBAMOYL-D-AMINO-ACID AMIDOHYDROLASE
 
Authors :  W. C. Wang, W. C. Chiu, J. Y. You
Date :  24 Mar 06  (Deposition) - 11 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  N-Carbamoyl-D-Amino-Acid Amidohydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Chiu, J. Y. You, J. S. Liu, S. K. Hsu, W. H. Hsu, C. H. Shih, J. K. Hwang, W. C. Wang
Structure-Stability-Activity Relationship In Covalently Cross-Linked N-Carbamoyl D-Amino Acid Amidohydrolase And N-Acylamino Acid Racemase.
J. Mol. Biol. V. 359 741 2006
PubMed-ID: 16650857  |  Reference-DOI: 10.1016/J.JMB.2006.03.063
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N-CARBAMOYL-D-AMINO ACID AMIDOHYDROLASE
    Chains: A, B, C, D
    EC Number: 3.5.1.77
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2GGK)

(-) Sites  (0, 0)

(no "Site" information available for 2GGK)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:302 -B:302
2C:302 -D:302

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Met A:73 -Pro A:74
2Met B:73 -Pro B:74
3Met C:73 -Pro C:74
4Met D:73 -Pro D:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CN_HYDROLASEPS50263 Carbon-nitrogen hydrolase domain profile.DCAS_RHIRD5-276
 
 
 		  4A:5-276
B:5-276
C:5-276
D:5-276

(-) Exons   (0, 0)

(no "Exon" information available for 2GGK)

(-) 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:302
 aligned with DCAS_RHIRD | Q44185 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:302
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  
           DCAS_RHIRD     3 RQMILAVGQQGPIARAETREQVVGRLLDMLTNAASRGVNFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFETAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPETWRVMGLKGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEEGCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKAHRQPQHYGLIAEF 304
               SCOP domains d2ggka1 A:3-304 N-carbamoyl-D-aminoacid amidohydrolase                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ggkA00 A:3-304  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........hhhhhhhhhhhhhhhhhhh...eee........hhhhh...hhhhhhhh.........hhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeee.....eeeeee..................hhhhhh........eeee..eeeeeee.hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..eee..eee....eee.....eeee......eeeeeeee...hhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CN_HYDROLASE  PDB: A:5-276 UniProt: 5-276                                                                                                                                                                                                                                       ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ggk A   3 RQMILAVGQQGPIARAETREQVVGRLLDMLTNAASRGVNFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFETAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPETWRVMGLKGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEEGCMLLGHSCIVAPTGEIVALTTTLEDEVITAALDLDRCRELREHIFNFKAHRQPQHYGLICEF 304
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  


Chain B from PDB  Type:PROTEIN  Length:302
 aligned with DCAS_RHIRD | Q44185 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:302
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  
           DCAS_RHIRD     3 RQMILAVGQQGPIARAETREQVVGRLLDMLTNAASRGVNFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFETAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPETWRVMGLKGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEEGCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKAHRQPQHYGLIAEF 304
               SCOP domains d2ggkb_ B: N-carbamoyl-D-aminoacid amidohydrolase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2ggkB00 B:3-304  [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.hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..eee..eee....eee.....eeee......eeeeeeee...hhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CN_HYDROLASE  PDB: B:5-276 UniProt: 5-276                                                                                                                                                                                                                                       ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ggk B   3 RQMILAVGQQGPIARAETREQVVGRLLDMLTNAASRGVNFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFETAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPETWRVMGLKGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEEGCMLLGHSCIVAPTGEIVALTTTLEDEVITAALDLDRCRELREHIFNFKAHRQPQHYGLICEF 304
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  


Chain C from PDB  Type:PROTEIN  Length:302
 aligned with DCAS_RHIRD | Q44185 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:302
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  
           DCAS_RHIRD     3 RQMILAVGQQGPIARAETREQVVGRLLDMLTNAASRGVNFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFETAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPETWRVMGLKGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEEGCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKAHRQPQHYGLIAEF 304
               SCOP domains d2ggkc_ C: N-carbamoyl-D-aminoacid amidohydrolase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2ggkC00 C:3-304  [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.hhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..eee..eee....eee.....eeee......eeeeeeee...hhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CN_HYDROLASE  PDB: C:5-276 UniProt: 5-276                                                                                                                                                                                                                                       ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ggk C   3 RQMILAVGQQGPIARAETREQVVGRLLDMLTNAASRGVNFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFETAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPETWRVMGLKGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEEGCMLLGHSCIVAPTGEIVALTTTLEDEVITAALDLDRCRELREHIFNFKAHRQPQHYGLICEF 304
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  


Chain D from PDB  Type:PROTEIN  Length:302
 aligned with DCAS_RHIRD | Q44185 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:302
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  
           DCAS_RHIRD     3 RQMILAVGQQGPIARAETREQVVGRLLDMLTNAASRGVNFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFETAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPETWRVMGLKGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEEGCMLLGHSCIVAPTGEIVALTTTLEDEVITAAVDLDRCRELREHIFNFKAHRQPQHYGLIAEF 304
               SCOP domains d2ggkd_ D: N-carbamoyl-D-aminoacid amidohydrolase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2ggkD00 D:3-304  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........hhhhhhhhhhhhhhhhhhh...eee........hhhhh...hhhhhhh..........hhhhhhhhhhhh.eeeeeeeeeee....eeeeeeeeee.....eeeeee..................hhhhhh........eeee..eeeee.hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eee..eee....eee.....eeee......eeeeeeee...hhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CN_HYDROLASE  PDB: D:5-276 UniProt: 5-276                                                                                                                                                                                                                                       ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ggk D   3 RQMILAVGQQGPIARAETREQVVGRLLDMLTNAASRGVNFIVFPELALTTFFPRWHFTDEAELDSFYETEMPGPVVRPLFETAAELGIGFNLGYAELVVEGGVKRRFNTSILVDKSGKIVGKYRKIHLPGHKEYEAYRPFQHLEKRYFEPGDLGFPVYDVDAAKMGMFICNDRRWPETWRVMGLKGAEIICGGYNTPTHNPPVPQHDHLTSFHHLLSMQAGSYQNGAWSAAAGKVGMEEGCMLLGHSCIVAPTGEIVALTTTLEDEVITAALDLDRCRELREHIFNFKAHRQPQHYGLICEF 304
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GGK)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DCAS_RHIRD | Q44185)
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2ggk)
 
  Sites
(no "Sites" information available for 2ggk)
 
  Cis Peptide Bonds
    Met A:73 - Pro A:74   [ RasMol ]  
    Met B:73 - Pro B:74   [ RasMol ]  
    Met C:73 - Pro C:74   [ RasMol ]  
    Met D:73 - Pro D:74   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ggk
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DCAS_RHIRD | Q44185
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.1.77
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DCAS_RHIRD | Q44185
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DCAS_RHIRD | Q44185: 1fo6 2ggl

(-) Related Entries Specified in the PDB File

1fo6 CRYSTAL STRUCTURE ANALYSIS OF N-CARBAMOYL-D-AMINO-ACID AMIDOHYDROLASE
2ggl THE SAME PROTEIN, A222C MUTANT