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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DIMETHYLARGININE DIMETHYLAMINOHYDROLASE-1 (DDAH-1) COVALENTLY BOUND WITH N5-(1-IMINOPENTYL)-L-ORNITHINE
 
Authors :  M. Lluis, Y. Wang, A. F. Monzingo, W. Fast, J. D. Robertus
Date :  13 Oct 10  (Deposition) - 10 Nov 10  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ddah, Nitric Oxide Synthase Regulation, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Lluis, Y. Wang, A. F. Monzingo, W. Fast, J. D. Robertus
Characterization Of C-Alkyl Amidines As Bioavailable Covalent Reversible Inhibitors Of Human Ddah-1.
Chemmedchem V. 6 81 2011
PubMed-ID: 20979083  |  Reference-DOI: 10.1002/CMDC.201000392

(-) Compounds

Molecule 1 - N(G),N(G)-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
    ChainsA, B
    EC Number3.5.3.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-HDDAH-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDDAH, DDAH1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDDAH-1, DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1, DDAHI, DIMETHYLARGININASE-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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1LN72Ligand/IonN~5~-[(1S)-1-AMINOPENTYL]-L-ORNITHINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1LN71Ligand/IonN~5~-[(1S)-1-AMINOPENTYL]-L-ORNITHINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1LN71Ligand/IonN~5~-[(1S)-1-AMINOPENTYL]-L-ORNITHINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:30 , ASP A:73 , PHE A:76 , GLU A:78 , ASP A:79 , ARG A:98 , GLY A:129 , ARG A:145 , HIS A:173 , VAL A:268 , ASP A:269 , CYS A:274BINDING SITE FOR RESIDUE LN7 A 286
2AC2SOFTWARELEU B:30 , ASP B:73 , PHE B:76 , GLU B:78 , ASP B:79 , ARG B:98 , GLY B:129 , HIS B:173 , VAL B:268 , ASP B:269 , GLY B:270 , CYS B:274 , HOH B:289BINDING SITE FOR RESIDUE LN7 B 286

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P8E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P8E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P8E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P8E)

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.10ENST0000028403110ENSE00001013010chr1:85930823-85930426398DDAH1_HUMAN1-1011012A:9-101 (gaps)
B:9-101 (gaps)
93
93
1.11aENST0000028403111aENSE00001663143chr1:85824530-85824431100DDAH1_HUMAN102-135342A:102-135
B:102-135
34
34
1.12ENST0000028403112ENSE00002130817chr1:85817262-8581718974DDAH1_HUMAN135-159252A:135-159
B:135-159
25
25
1.13ENST0000028403113ENSE00002113532chr1:85816217-85816098120DDAH1_HUMAN160-199402A:160-199
B:160-199
40
40
1.14bENST0000028403114bENSE00002116891chr1:85790566-85790423144DDAH1_HUMAN200-247482A:200-247
B:200-247
48
48
1.15bENST0000028403115bENSE00001928014chr1:85787251-857841683084DDAH1_HUMAN248-285382A:248-282
B:248-282
35
35

(-) 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_HUMAN | O94760 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:274
                                    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_HUMAN     9 AFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKK 282
               SCOP domains d3p8ea_ A: automated mat  ches                                                                                                                                                                                                                                                     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..eeeee.hhhhhhhhhhhhhh.....eeeee.hhhhhh.eeeee...eeeeee.....hhhhhhhhh....eeeee..hhhhhhh...hhhhheee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:9-101 (gaps) UniProt: 1-101 [INCOMPLETE]                                   Exon 1.11a  PDB: A:102-135        ------------------------Exon 1.13  PDB: A:160-199               Exon 1.14b  PDB: A:200-247 UniProt: 200-247     Exon 1.15b  PDB: A:248-282          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:135-159--------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3p8e A   9 AFGRATHAVVRALPESLGQHALRS--GEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKK 282
                                    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    
                                                  32 35                                                                                                                                                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:272
 aligned with DDAH1_HUMAN | O94760 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:274
                                    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_HUMAN     9 AFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKK 282
               SCOP domains d3p8eb_ B: automated mat  ches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Amidinotransf-3p8eB01   B:12-281                                                                                                                                                                                                                                              - Pfam domains (1)
           Pfam domains (2) ---Amidinotransf-3p8eB02   B:12-281                                                                                                                                                                                                                                              - Pfam domains (2)
         Sec.struct. author ......eeeee....hhhhhh...--....hhhhhhhhhhhhhhhhhh....eeeee...........hhh.eeee..eeee....hhhhhhhhhhhhhhhhh...eeee........hhh.eee....eeeee....hhhhhhhhhhhh....eeeee.....hhhh.eeeee..eeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhh.eeeee...eeeeee.....hhhhhhhhh....eeeee....hhhhhh..hhhhheee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: B:9-101 (gaps) UniProt: 1-101 [INCOMPLETE]                                   Exon 1.11a  PDB: B:102-135        ------------------------Exon 1.13  PDB: B:160-199               Exon 1.14b  PDB: B:200-247 UniProt: 200-247     Exon 1.15b  PDB: B:248-282          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: B:135-159--------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3p8e B   9 AFGRATHAVVRALPESLGQHALRS--GEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKK 282
                                    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    
                                                  32 35                                                                                                                                                                                                                                                       

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P8E)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GME (20)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DDAH1_HUMAN | O94760)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
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:0006525    arginine metabolic process    The chemical reactions and pathways involving 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:0007263    nitric oxide mediated signal transduction    Any intracellular signal transduction in which the signal is passed on within the cell via nitric oxide (NO). Includes synthesis of nitric oxide, receptors/sensors for nitric oxide (such as soluble guanylyl cyclase/sGC) and downstream effectors that further transmit the signal within the cell. Nitric oxide transmits its downstream effects through either cyclic GMP (cGMP)-dependent or independent mechanisms.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    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:0050999    regulation of nitric-oxide synthase activity    Any process that modulates the activity of the enzyme nitric-oxide synthase.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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_HUMAN | O947602jai 2jaj 3i2e 3i4a 3p8p

(-) Related Entries Specified in the PDB File

3i2e HUMAN DDAH-1
3i4a HUMAN DDAH-1 BOUND WITH N5-(1-IMINOPROPYL)-L-ORNITHINE
3p8p HUMAN DDAH-1 BOUND WITH N5-(1-IMINOPENTYL)-L-ORNITHINE