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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMETHYLARGININE DIMETHYLAMINOHYDROLASE H162G ADDUCT WITH S-METHYL-L-THIOCITRULLINE
 
Authors :  A. F. Monzingo, T. W. Linsky, E. M. Stone, W. Fast, J. D. Robertus
Date :  18 Dec 07  (Deposition) - 17 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Enzyme Adduct, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. W. Linsky, A. F. Monzingo, E. M. Stone, J. D. Robertus, W. Fast
Promiscuous Partitioning Of A Covalent Intermediate Common In The Pentein Superfamily.
Chem. Biol. V. 15 467 2008
PubMed-ID: 18482699  |  Reference-DOI: 10.1016/J.CHEMBIOL.2008.03.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIMETHYLARGININE DIMETHYLAMINOHYDROLASE
    Chains: A, B
    EC Number: 3.5.3.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: PA1195
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SMZ2Ligand/IonN~5~-[(E)-IMINO(METHYLSULFANYL)METHYL]-L-ORNITHINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SMZ1Ligand/IonN~5~-[(E)-IMINO(METHYLSULFANYL)METHYL]-L-ORNITHINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SMZ1Ligand/IonN~5~-[(E)-IMINO(METHYLSULFANYL)METHYL]-L-ORNITHINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:18 , ASP A:60 , PHE A:63 , GLU A:65 , ASP A:66 , ARG A:85 , GLY A:116 , ARG A:132 , ILE A:243 , ASP A:244 , CYS A:249BINDING SITE FOR RESIDUE SMZ A 500
2AC2SOFTWARELEU B:18 , ASP B:60 , PHE B:63 , GLU B:65 , ASP B:66 , ARG B:85 , GLY B:116 , ARG B:132 , ILE B:243 , ASP B:244 , CYS B:249BINDING SITE FOR RESIDUE SMZ B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BPB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:109 -Pro A:110
2Ala B:109 -Pro B:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BPB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BPB)

(-) Exons   (0, 0)

(no "Exon" information available for 3BPB)

(-) 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:254
 aligned with DDAH_PSEAE | Q9I4E3 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:254
                                    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    
           DDAH_PSEAE     1 MFKHIIARTPARSLVDGLTSSHLGKPDYAKALEQHNAYIRALQTCDVDITLLPPDERFPDSVFVEDPVLCTSRCAIITRPGAESRRGETEIIEETVQRFYPGKVERIEAPGTVEAGDIMMVGDHFYIGESARTNAEGARQMIAILEKHGLSGSVVRLEKVLHLKTGLAYLEHNNLLAAGEFVSKPEFQDFNIIEIPEEESYAANCIWVNERVIMPAGYPRTREKIARLGYRVIEVDTSEYRKIDGGVSCMSLRF 254
               SCOP domains d3bpba_ A: Dimethylarginine dimethylaminohydrolase DDAH                                                                                                                                                                                                        SCOP domains
               CATH domains 3bpbA00 A:1-254 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhh.........hhhhhhhhhhhhhhhhh....eeeee.....hhhhhh....eee....eee....hhhhhhhhh.hhhhhhhhh...eee.......hhh.eeee..eeeee.....hhhhhhhhhhhhhhh.....ee......hhhh.eee....eeeee.hhhhhhhhh..eeeeehhhhhhhhh.eee..eeeee..hhhhhhhhhhh..eeeee.hhhhhh.........eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bpb A   1 MFKHIIARTPARSLVDGLTSSHLGKPDYAKALEQHNAYIRALQTCDVDITLLPPDERFPDSVFVEDPVLCTSRCAIITRPGAESRRGETEIIEETVQRFYPGKVERIEAPGTVEAGDIMMVGDHFYIGESARTNAEGARQMIAILEKHGLSGSVVRLEKVLGLKTGLAYLEHNNLLAAGEFVSKPEFQDFNIIEIPEEESYAANCIWVNERVIMPAGYPRTREKIARLGYRVIEVDTSEYRKIDGGVSCMSLRF 254
                                    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    


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with DDAH_PSEAE | Q9I4E3 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:254
                                    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    
           DDAH_PSEAE     1 MFKHIIARTPARSLVDGLTSSHLGKPDYAKALEQHNAYIRALQTCDVDITLLPPDERFPDSVFVEDPVLCTSRCAIITRPGAESRRGETEIIEETVQRFYPGKVERIEAPGTVEAGDIMMVGDHFYIGESARTNAEGARQMIAILEKHGLSGSVVRLEKVLHLKTGLAYLEHNNLLAAGEFVSKPEFQDFNIIEIPEEESYAANCIWVNERVIMPAGYPRTREKIARLGYRVIEVDTSEYRKIDGGVSCMSLRF 254
               SCOP domains d3bpbb_ B: Dimethylarginine dimethylaminohydrolase DDAH                                                                                                                                                                                                        SCOP domains
               CATH domains 3bpbB00 B:1-254 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhh.........hhhhhhhhhhhhhhhhh....eeeee.....hhhhhh....eee....eee....hhhhhhhhhhhhhhhhhhh...eee.......hhh.eeee..eeeee.....hhhhhhhhhhhhhhh.....ee......hhhh.eee....eeeee.hhhhhhhhh..eeeeehhhhhhhhh.eee..eeeee..hhhhhhhhhhh..eeeee.hhhhhh.........eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bpb B   1 MFKHIIARTPARSLVDGLTSSHLGKPDYAKALEQHNAYIRALQTCDVDITLLPPDERFPDSVFVEDPVLCTSRCAIITRPGAESRRGETEIIEETVQRFYPGKVERIEAPGTVEAGDIMMVGDHFYIGESARTNAEGARQMIAILEKHGLSGSVVRLEKVLGLKTGLAYLEHNNLLAAGEFVSKPEFQDFNIIEIPEEESYAANCIWVNERVIMPAGYPRTREKIARLGYRVIEVDTSEYRKIDGGVSCMSLRF 254
                                    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
   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 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 3BPB)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DDAH_PSEAE | Q9I4E3)
molecular function
    GO:0016403    dimethylargininase activity    Catalysis of the reaction: N(G),N(G)-dimethyl-L-arginine + H2O = dimethylamine + L-citrulline.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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        DDAH_PSEAE | Q9I4E3: 1h70 3rhy

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