3LFV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF UNLIGANDED PDE5A GAF DOMAIN

Authors :   H. Wang, H. Robinson, H. Ke

Date :   18 Jan 10 (Deposition) - 22 Sep 10 (Release) - 05 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Gaf, Cgmp Signaling, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wang, H. Robinson, H. Ke
Conformation Changes, N-Terminal Involvement, And Cgmp Signal Relay In The Phosphodiesterase-5 Gaf Domain.
J. Biol. Chem. V. 285 38149 2010
PubMed-ID: 20861010 | Reference-DOI: 10.1074/JBC.M110.141614

Molecule 1 - CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE
	Chains	:	A, B
	EC Number	:	3.1.4.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A (MODIFIED)
	Expression System Strain	:	BL21(CODONPLUS)
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 98-518
	Gene	:	PDE5, PDE5A, PDE5A1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE, CGB-PDE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3LFV)

(no "Site" information available for 3LFV)

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

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

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_027776	S	181	A	PDE5A_HUMAN	Polymorphism	17051276	A/B	S	181	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

Asymmetric/Biological Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000354960	1a	ENSE00001851914	chr4:120550146-120549675	472	PDE5A_HUMAN	1-51	51	2	A:90-92 B:90-92	3 3
1.4	ENST00000354960	4	ENSE00001637089	chr4:120528452-120527864	589	PDE5A_HUMAN	51-247	197	2	A:92-247 (gaps) B:92-247 (gaps)	197 197
1.5b	ENST00000354960	5b	ENSE00000935544	chr4:120517767-120517678	90	PDE5A_HUMAN	248-277	30	2	A:248-277 B:248-277	30 30
1.6	ENST00000354960	6	ENSE00000970323	chr4:120488299-120488228	72	PDE5A_HUMAN	278-301	24	2	A:278-301 B:278-301	24 24
1.7	ENST00000354960	7	ENSE00000970324	chr4:120486565-120486476	90	PDE5A_HUMAN	302-331	30	2	A:302-331 B:302-331	30 30
1.8b	ENST00000354960	8b	ENSE00000970325	chr4:120484125-120483988	138	PDE5A_HUMAN	332-377	46	2	A:332-377 B:332-377	46 46
1.9	ENST00000354960	9	ENSE00000970326	chr4:120481518-120481451	68	PDE5A_HUMAN	378-400	23	2	A:378-394 B:378-394	17 17
1.10	ENST00000354960	10	ENSE00000970327	chr4:120474901-120474793	109	PDE5A_HUMAN	400-436	37	2	A:407-435 B:409-434	29 26
1.11a	ENST00000354960	11a	ENSE00000970328	chr4:120473792-120473705	88	PDE5A_HUMAN	437-466	30	2	A:446-466 B:447-466	21 20
1.13	ENST00000354960	13	ENSE00000935541	chr4:120463789-120463614	176	PDE5A_HUMAN	466-524	59	2	A:466-520 B:466-520	55 55
1.15b	ENST00000354960	15b	ENSE00000935545	chr4:120460174-120460115	60	PDE5A_HUMAN	525-544	20	0	-	-
1.18	ENST00000354960	18	ENSE00001016848	chr4:120446850-120446704	147	PDE5A_HUMAN	545-593	49	0	-	-
1.19b	ENST00000354960	19b	ENSE00001016844	chr4:120442215-120442090	126	PDE5A_HUMAN	594-635	42	0	-	-
1.20c	ENST00000354960	20c	ENSE00001016846	chr4:120440294-120440200	95	PDE5A_HUMAN	636-667	32	0	-	-
1.22	ENST00000354960	22	ENSE00001016843	chr4:120432289-120432202	88	PDE5A_HUMAN	667-696	30	0	-	-
1.23b	ENST00000354960	23b	ENSE00001016840	chr4:120428859-120428759	101	PDE5A_HUMAN	697-730	34	0	-	-
1.24b	ENST00000354960	24b	ENSE00001016847	chr4:120427087-120427010	78	PDE5A_HUMAN	730-756	27	0	-	-
1.25	ENST00000354960	25	ENSE00001016842	chr4:120425754-120425691	64	PDE5A_HUMAN	756-777	22	0	-	-
1.26a	ENST00000354960	26a	ENSE00001016841	chr4:120423810-120423736	75	PDE5A_HUMAN	778-802	25	0	-	-
1.27a	ENST00000354960	27a	ENSE00001016845	chr4:120422408-120422325	84	PDE5A_HUMAN	803-830	28	0	-	-
1.28c	ENST00000354960	28c	ENSE00001890486	chr4:120419893-120415550	4344	PDE5A_HUMAN	831-875	45	0	-	-

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:391
 aligned with PDE5A_HUMAN | O76074 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:472
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518  
          PDE5A_HUMAN    49 ATREMVNAWFAERVHTIPVCKEGIRGHTESCSCPLQQSPRADNSAPGTPTRKISASEFDRPLRPIVVKDSEGTVSFLSDSEKKEQMPLTPPRFDHDEGDQCSRLLELVKDISSHLDVTALCHKIFLHIHGLISADRYSLFLVCEDSSNDKFLISRLFDVAEGSTLEEVSNNCIRLEWNKGIVGHVAALGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAAYLAFCGIVLHNAQLYETSLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKSSDTLTREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFPWTTENTGNVNQQCIRSLLCTPIKNGKKNKVIGVCQLVNKMEENTGKVKPFNRNDEQFLEAFVIFCGLGIQNTQMYEAVERAMAKQM 520
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh-----------------------------------------hhhhhhhhhhhh.......eee...eee....------------------.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeeeeeeeee.....eeeeeeee...............eeee..hhhhhhhhhhh..eee.hhhhh....hhhhhhhh.....eeeeeee.....eeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeeee..........eeeeee...eee.------------..hhhhhhhhhhh..eee...........----------.....eeeeeee......eeeeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5b  PDB: A:248-277     Exon 1.6  PDB: A:278-301Exon 1.7  PDB: A:302-331      Exon 1.8b  PDB: A:332-377 UniProt: 332-377    ----------------------Exon 1.10  PDB: A:407-435            Exon 1.11a  PDB: A:446-466    ------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --Exon 1.4  PDB: A:92-247 (gaps) UniProt: 51-247                                                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:378-39-----------------------------------------------------------------Exon 1.13  PDB: A:466-520 UniProt: 466-524 [INCOMPLETE] Transcript 1 (2)
                 3lfv A  90 AMEHMA-----------------------------------------SMTRKISASEFDRPLRPIVVKDSEGTVSFLSD------------------GDQSSRLLELVKDISSHLDVTALCHKIFLHIHGLISADRYSLFLVCEDSSNDKFLISRLFDVAEGSTLEEVSNNCIRLEWNKGIVGHVAALGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAAYLAFCGIVLHNAQLYETSLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKS------------INYMYAQYVKNTMEPLNIPDVSKDKRFPW----------QCIRSLLCTPIKNGKKNKVIGVCQLVNKMEENTGKVKPFNRNDEQFLEAFVIFCGLGIQNTQMYEAVERAMAKRN 520
                                 |   -         -         -         -       |98       108       118        |-         -       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388     |   -       408       418       428      |  -       448       458       468       478       488       498       508       518  
                                95                                        96                            127                146                                                                                                                                                                                                                                                     394          407                         435        446

Chain B from PDB  Type:PROTEIN  Length:380
 aligned with PDE5A_HUMAN | O76074 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:472
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518  
          PDE5A_HUMAN    49 ATREMVNAWFAERVHTIPVCKEGIRGHTESCSCPLQQSPRADNSAPGTPTRKISASEFDRPLRPIVVKDSEGTVSFLSDSEKKEQMPLTPPRFDHDEGDQCSRLLELVKDISSHLDVTALCHKIFLHIHGLISADRYSLFLVCEDSSNDKFLISRLFDVAEGSTLEEVSNNCIRLEWNKGIVGHVAALGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAAYLAFCGIVLHNAQLYETSLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKSSDTLTREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFPWTTENTGNVNQQCIRSLLCTPIKNGKKNKVIGVCQLVNKMEENTGKVKPFNRNDEQFLEAFVIFCGLGIQNTQMYEAVERAMAKQM 520
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------                                         -----------------------------------                --------------------------------------------------------------         --------------------------------------------------------------------------------------------------------------------------------GAF-3lfvB01 B:346-503                                                                                                                                         ----------------- Pfam domains (1)
           Pfam domains (2) ------                                         -----------------------------------                --------------------------------------------------------------         --------------------------------------------------------------------------------------------------------------------------------GAF-3lfvB02 B:346-503                                                                                                                                         ----------------- Pfam domains (2)
           Pfam domains (3) ------                                         -----------------------------------                --------------------------------------------------------------         --------------------------------------------------------------------------------------------------------------------------------GAF-3lfvB03 B:346-503                                                                                                                                         ----------------- Pfam domains (3)
           Pfam domains (4) ------                                         -----------------------------------                --------------------------------------------------------------         --------------------------------------------------------------------------------------------------------------------------------GAF-3lfvB04 B:346-503                                                                                                                                         ----------------- Pfam domains (4)
         Sec.struct. author .hhhhh-----------------------------------------...................ee.....ee.......----------------hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeeeeeeee.....eeeeeeee...---------...eee...hhhhhhhhhhh..eee.hhhhh....hhhhhhhh.....eeeeeee.....eeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeeee..........eeeeee.......--------------.hhhhhhhhhh..eee..........------------....eeeeee.........eeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5b  PDB: B:248-277     Exon 1.6  PDB: B:278-301Exon 1.7  PDB: B:302-331      Exon 1.8b  PDB: B:332-377 UniProt: 332-377    ----------------------Exon 1.10  PDB: B:409-434            Exon 1.11a  PDB: B:447-466    ------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --Exon 1.4  PDB: B:92-247 (gaps) UniProt: 51-247                                                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: B:378-39-----------------------------------------------------------------Exon 1.13  PDB: B:466-520 UniProt: 466-524 [INCOMPLETE] Transcript 1 (2)
                 3lfv B  90 AMEHMA-----------------------------------------SMTRKISASEFDRPLRPIVVKDSEGTVSFLSDSEK----------------DQSSRLLELVKDISSHLDVTALCHKIFLHIHGLISADRYSLFLVCEDSSNDKFLISRLFDVA---------NNCIRLEWNKGIVGHVAALGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAAYLAFCGIVLHNAQLYETSLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKS--------------YMYAQYVKNTMEPLNIPDVSKDKRFP------------CIRSLLCTPIKNGKKNKVIGVCQLVNKMEENTGKVKPFNRNDEQFLEAFVIFCGLGIQNTQMYEAVERAMAKRN 520
                                 |   -         -         -         -       |98       108       118       128 |       -       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388     |   -         -|      418       428     |   -       448       458       468       478       488       498       508       518  
                                95                                        96                               130              147                                                          208       218                                                                                                                                                                             394            409                      434          447

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 '\|'

(no "SCOP Domain" information available for 3LFV)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GAF (44)

Family: GAF (30)

Homo sapiens (Human) (4)

1a	GAF-3lfvB01	B:346-503
1b	GAF-3lfvB02	B:346-503
1c	GAF-3lfvB03	B:346-503
1d	GAF-3lfvB04	B:346-503

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDE5A_HUMAN | O76074)

molecular function
	GO:0047555	3',5'-cyclic-GMP phosphodiesterase activity	Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
	GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
	GO:0030553	cGMP binding	Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
	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:0004112	cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside phosphate.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
	GO:0046069	cGMP catabolic process	The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate.
	GO:0046068	cGMP metabolic process	The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0042130	negative regulation of T cell proliferation	Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
	GO:0055118	negative regulation of cardiac muscle contraction	Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction.
	GO:0043406	positive regulation of MAP kinase activity	Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
	GO:0010613	positive regulation of cardiac muscle hypertrophy	Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
	GO:0060282	positive regulation of oocyte development	Any process that increases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
	GO:0030823	regulation of cGMP metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cGMP.
	GO:0055119	relaxation of cardiac muscle	The process in which the extent of cardiac muscle contraction is reduced.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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(no "Sites" information available for 3lfv)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lfv)

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	3lfv
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Exons (10, 20)

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