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(-) Description

Title :  CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I IN COMPLEX WITH L-HOMOCYSTEINE
 
Authors :  D. Frey, O. Braun, C. Briand, M. Vasak, M. G. Grutter
Date :  17 Mar 06  (Deposition) - 17 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nos Regulation, S-Nitrosylation, Zinc, Hydrolase, No, Mma, Adma, Acetylation, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Frey, O. Braun, C. Briand, M. Vasak, M. G. Grutter
Structure Of The Mammalian Nos Regulator Dimethylarginine Dimethylaminohydrolase: A Basis For The Design Of Specific Inbitors
Structure V. 14 901 2006
PubMed-ID: 16698551  |  Reference-DOI: 10.1016/J.STR.2006.03.006

(-) Compounds

Molecule 1 - NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
    Chains: A, B
    EC Number: 3.5.3.18
    Organ: BRAIN
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I, DIMETHYLARGININASE 1, DDAHI, DDAH-1

 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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2HCS2Ligand/Ion2-AMINO-4-MERCAPTO-BUTYRIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CIT-1Ligand/IonCITRIC ACID
2HCS1Ligand/Ion2-AMINO-4-MERCAPTO-BUTYRIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2HCS1Ligand/Ion2-AMINO-4-MERCAPTO-BUTYRIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:29 , ASP A:72 , PHE A:75 , ASP A:78 , ARG A:97 , ARG A:144 , VAL A:267 , ASP A:268 , CYS A:273 , HOH A:2316BINDING SITE FOR RESIDUE HCS A1281
2AC2SOFTWARELEU B:29 , ASP B:72 , PHE B:75 , ASP B:78 , ARG B:97 , ARG B:144 , VAL B:267 , ASP B:268 , CYS B:273 , HOH B:2308BINDING SITE FOR RESIDUE HCS B1281
3AC3SOFTWARELYS A:195 , ILE A:199 , HOH A:2217 , ARG B:41 , ARG B:44 , GLN B:45 , LEU B:48 , SER B:260 , HOH B:2279 , HOH B:2318BINDING SITE FOR RESIDUE CIT B1282

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CI5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CI5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CI5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CI5)

(-) Exons   (0, 0)

(no "Exon" information available for 2CI5)

(-) 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:272
 aligned with DDAH1_BOVIN | P56965 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:272
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279  
          DDAH1_BOVIN    10 FGRATHVVVRALPESLAQQALRRTKGDEVDFARAERQHQLYVGVLGSKLGLQVVQLPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEADMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVVDALHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDTAANCIYLNIPSKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSNSELEKVDGLLTCSSVLINK 281
               SCOP domains d2ci5a_ A: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhh.........hhhhhhhhhhhhhhhhhh....eeeee..........hhhh.eeee..eeee....hhhhhhhhhhhhhhhhhh..eeee........hhh.eee....eeeee....hhhhhhhhhhhh....eeeee.....hhhh.eeeee..eeee..hhhhhhhhhhhhhhh....eeee..hhhhhh.eeeee...eeeeee.....hhhhhhhhhh....eeee..hhhhhh....hhhhheee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ci5 A   9 FGRATHVVVRALPESLAQQALRRTKGDEVDFARAERQHQLYVGVLGSKLGLQVVQLPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEADMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVVDALHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDTAANCIYLNIPSKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSNSELEKVDGLLTCSSVLINK 280
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278  


Chain B from PDB  Type:PROTEIN  Length:273
 aligned with DDAH1_BOVIN | P56965 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:273
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278   
          DDAH1_BOVIN     9 TFGRATHVVVRALPESLAQQALRRTKGDEVDFARAERQHQLYVGVLGSKLGLQVVQLPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEADMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVVDALHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDTAANCIYLNIPSKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSNSELEKVDGLLTCSSVLINK 281
               SCOP domains d2ci5b_ B: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....hhhhhh.........hhhhhhhhhhhhhhhhhh....eeeee..........hhhh.eeee..eeee....hhhhhhhhhhhhhhhhhh..eeee........hhh.eee...eeeeee....hhhhhhhhhhhh...eeeeee.....hhhh.eeeee..eeee..hhhhhhhhhhhhhhh....eeee..hhhhhh.eeeee...eeeeee.....hhhhhhhhhh....eeee..hhhhhh....hhhhheee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ci5 B   8 TFGRATHVVVRALPESLAQQALRRTKGDEVDFARAERQHQLYVGVLGSKLGLQVVQLPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEADMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVVDALHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDTAANCIYLNIPSKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSNSELEKVDGLLTCSSVLINK 280
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277
   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  (0, 0)

(no "CATH Domain" information available for 2CI5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CI5)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DDAH1_BOVIN | P56965)
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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006527    arginine catabolic process    The chemical reactions and pathways resulting in the breakdown of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0000052    citrulline metabolic process    The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins.
    GO:0006809    nitric oxide biosynthetic process    The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
    GO:0045429    positive regulation of nitric oxide biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
    GO:0017014    protein nitrosylation    The covalent addition of a nitric oxide group to an amino acid within a protein.
    GO:0003073    regulation of systemic arterial blood pressure    The process that modulates the force with which blood travels through the systemic arterial circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DDAH1_BOVIN | P56965: 2c6z 2ci1 2ci3 2ci4 2ci6 2ci7

(-) Related Entries Specified in the PDB File

2c6z CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I IN COMPLEX WITH CITRULLINE
2ci1 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I IN COMPLEX WITH S- NITROSO-LHOMOCYSTEINE
2ci3 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE CRYSTAL FORM I
2ci4 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I CRYSTAL FORM II
2ci6 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I BOUND WITH ZINC LOW PH
2ci7 CRYSTAL STRUCTURE OF DIMETHYLARGININE DIMETHYLAMINOHYDROLASE I IN COMPLEX WITH ZINC , HIGH PH