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Title :   DDAH1 COMPLEXED WITH CITRULLINE

Authors :   J. Murray-Rust, B. P. O'Hara, S. Rossiter, J. M. Leiper, P. Vallance, N. Q. Mcdonald

Date :   29 Nov 06 (Deposition) - 13 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Ddah, Hydrolase, Nitric Oxide Synthase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Leiper, M. Nandi, B. Torondel, J. Murray-Rust, M. Malaki, B. O'Hara S. Rossiter, S. Anthony, M. Madhani, D. Selwood, C. Smith, B. Wojciak-Stothard, A. Rudiger, R. Stidwill, N. Q. Mcdonald, P. Vallance
Disruption Of Methylarginine Metabolism Impairs Vascular Homeostasis.
Nat. Med. (N. Y. ) V. 13 198 2007
PubMed-ID: 17273169 | Reference-DOI: 10.1038/NM1543

Molecule 1 - NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1
	Chains	:	A, B
	EC Number	:	3.5.3.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	B834(DE3)
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DIMETHYLARGININASE-1, DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1, DDAHI, DDAH-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 18)

No.	Name	Count	Type	Full Name
1	CIR	1	Ligand/Ion	CITRULLINE
2	MSE	17	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	CIR	1	Ligand/Ion	CITRULLINE
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 9)

No.	Name	Count	Type	Full Name
1	CIR	-1	Ligand/Ion	CITRULLINE
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:29 , ASP A:72 , GLU A:77 , ASP A:78 , ARG A:97 , GLY A:128 , ARG A:144 , HIS A:172 , VAL A:267 , ASP A:268 , LEU A:270 , CYS A:273 , HOH A:2114	BINDING SITE FOR RESIDUE CIR A1281

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

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

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

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

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.10	ENST00000284031	10	ENSE00001013010	chr1:85930823-85930426	398	DDAH1_HUMAN	1-101	101	2	A:8-100 B:0-100	93 101
1.11a	ENST00000284031	11a	ENSE00001663143	chr1:85824530-85824431	100	DDAH1_HUMAN	102-135	34	2	A:101-134 B:101-134 (gaps)	34 34
1.12	ENST00000284031	12	ENSE00002130817	chr1:85817262-85817189	74	DDAH1_HUMAN	135-159	25	2	A:134-158 B:134-158 (gaps)	25 25
1.13	ENST00000284031	13	ENSE00002113532	chr1:85816217-85816098	120	DDAH1_HUMAN	160-199	40	2	A:159-198 (gaps) B:159-198 (gaps)	40 40
1.14b	ENST00000284031	14b	ENSE00002116891	chr1:85790566-85790423	144	DDAH1_HUMAN	200-247	48	2	A:199-246 B:199-246 (gaps)	48 48
1.15b	ENST00000284031	15b	ENSE00001928014	chr1:85787251-85784168	3084	DDAH1_HUMAN	248-285	38	2	A:247-280 B:247-280	34 34

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:271
 aligned with DDAH1_HUMAN | O94760 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_HUMAN     9 AFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINK 281
               SCOP domains d2jaia_ 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...eeeeee....hhhhhhhhhhhh...eeeeee.--..hhhh.eeeee..eeee..hhhhhhhhhhhhhh.....eeee...hhhhh.eeeee...eeeeee.....hhhhhhhhh....eeeee..hhhhhh....hhhhheee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:8-100 UniProt: 1-101 [INCOMPLETE]                                          Exon 1.11a  PDB: A:101-134        ------------------------Exon 1.13  PDB: A:159-198 (gaps)        Exon 1.14b  PDB: A:199-246 UniProt: 200-247     Exon 1.15b  PDB: A:247-280         Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:134-158-------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2jai A   8 AFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDmmKEALEKLQLNIVEmKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPV--GLHLKSFCSmAGPNLIAIGSSESAQKALKImQQmSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHmLIPVSmSELEKVDGLLTCCSVLINK 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   
                                                                                                                         103-MSE        118-MSE                                          167  |      179-MSE              200-MSE                                                255-MSE |                   
                                                                                                                          104-MSE                                                           170                              203-MSE                                                   261-MSE

Chain B from PDB  Type:PROTEIN  Length:271
 aligned with DDAH1_HUMAN | O94760 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:285
                                1                                                                                                                                                                                                                                                                                        
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276     
          DDAH1_HUMAN     - ----MAGLGHPAAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINK 281
               SCOP domains d2jaib_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...............eeeee....hhhhhh.........hhhhhhhhhhhhhhhhhh....eeeee..........hhhh.eeee..eeee....hhhhhhhhhhhhhhhhhh..eeee..--....hhh.ee...--.eeee....hhhhhhhhhhhh.....eeee.---.hhhhh.eeee..eeee--..hhhhhhhhhhhh---..eeee..hhhhhh.eeeee...eeeeeee...--..hhhhhh....eeeeee.hhhhhh....hhhhheee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ----Exon 1.10  PDB: B:0-100 UniProt: 1-101                                                               Exon 1.11a  PDB: B:101-134 (gaps) ------------------------Exon 1.13  PDB: B:159-198 (gaps)        Exon 1.14b  PDB: B:199-246 (gaps)               Exon 1.15b  PDB: B:247-280         Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------Exon 1.12                -------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2jai B  -4 GPLGmAGLGHPAAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDmmKEALEKLQLNIVEmK--NATLDGGDVLFTG--FFVGLSKRTNQRGAEILADTFKDYAVSTVPV---LHLKSFCSmAGPNLIAI--SESAQKALKImQQm---RYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPE--PESAKVYEKLKDHmLIPVSmSELEKVDGLLTCCSVLINK 280
                                |    5        15        25        35        45        55        65        75        85        95       105       115  ||  |125        |- |     145       155       165 |   | 175   |   185 |  |  195    |  | - |     215       225       235   |  |245       255     | 265       275     
                                0-MSE                                                                                                103-MSE        118-MSE         134  |                           167 171     179-MSE 187  |       200-MSE207                             239  |          255-MSE |                   
                                                                                                                                      104-MSE        119  |            137                                                  190          203-MSE                                242                261-MSE               
                                                                                                                                                        122

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Pentein, beta/alpha-propeller (68)

Superfamily: Pentein (68)

Family: automated matches (17)

Protein domain: automated matches (17)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d2jaia_	A:
1b	d2jaib_	B:

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

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

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.

Asymmetric Unit
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	3.5.3.18
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	DDAH1_HUMAN \| O94760	:	2jaj 3i2e 3i4a 3p8e 3p8p

1h70	DDAH FROM PSEUDOMONAS AERUGINOSA. C249S MUTANT COMPLEXED WITH CITRULLINE
2jaj	DDAH1 COMPLEXED WITH L-257

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 18)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (6, 12)

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Gene Ontology (16, 16)

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