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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN SOLUBLE GUANYLATE CYCLASE 1 BETA 3.

Authors :   C. K. Allerston, C. D. O. Cooper, J. Muniz, A. C. W. Pike, F. Von Delft, C. H. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, O. Gileadi

Date :   23 Nov 09 (Deposition) - 01 Dec 09 (Release) - 10 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

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

Keywords :   Lyase, Gucy1, Metal-Binding, Cgmp Biosynthesis, Nucleotide-Binding, Cyclase, Gucy1B3, Gtp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. K. Allerston, F. Von Delft, O. Gileadi
Crystal Structures Of The Catalytic Domain Of Human Soluble Guanylate Cyclase.
Plos One V. 8 57644 2013
PubMed-ID: 23505436 | Reference-DOI: 10.1371/JOURNAL.PONE.0057644

Molecule 1 - GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-1
	Chains	:	A, B
	EC Number	:	4.6.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-CTHF
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3 PRARE2
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 994-1205
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GUANYLATE CYCLASE 1 BETA 3, GCS-BETA-1, SOLUBLE GUANYLATE CYCLASE SMALL SUBUNIT, GCS-BETA-3

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE B:468 , GLY B:484 , LEU B:485 , PRO B:486 , GLU B:487	BINDING SITE FOR RESIDUE EDO B1609
2	AC2	SOFTWARE	PHE A:468 , ARG A:494 , SER A:495 , HOH A:2056	BINDING SITE FOR RESIDUE EDO A1611
3	AC3	SOFTWARE	VAL A:428 , GLY A:429 , PHE A:430 , PHE A:433 , VAL A:517 , HOH A:2162	BINDING SITE FOR RESIDUE EDO A1612

(no "SS Bond" information available for 2WZ1)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:485	-	Pro A:486
2	Leu B:485	-	Pro B:486

(no "SAP(SNP)/Variant" information available for 2WZ1)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GUANYLATE_CYCLASE_2	PS50125	Guanylate cyclase domain profile.	GCYB1_HUMAN	421-554	2	A:421-554 B:421-554
2	GUANYLATE_CYCLASE_1	PS00452	Guanylate cyclase signature.	GCYB1_HUMAN	531-554	2	A:531-554 B:531-554

(no "Exon" information available for 2WZ1)

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:197
 aligned with GCYB1_HUMAN | Q02153 from UniProtKB/Swiss-Prot  Length:619

    Alignment length:199
                                   421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601         
          GCYB1_HUMAN   412 VPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCLMSPENSDPQFHLEHRGPVSMKGKKEPMQVWFLSRKNTG 610
               SCOP domains d2wz1a_ A: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee.hhhhhhhhh..--hhhhhhhhhhhhhhhhhhhhh.......eee......eeeee.......hhhhhhhhhhhhhhhhhh..ee..ee..eeeeeeeeeeeeeee.....eeeeehhhhhhhhhhhhh.....eeeehhhhhhh.........eeeeeeeee........eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------GUANYLATE_CYCLASE_2  PDB: A:421-554 UniProt: 421-554                                                                                  -------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------GUANYLATE_CYCLASE_1     -------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wz1 A 412 VPAKRYDNVTILFSGIVGFNAFCSKHAS--GAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCLMSPENSDPQFHLEHRGPVSMKGKKEPMQVWFLSRKNTG 610
                                   421       431       | -|      451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601         
                                                     439  |                                                                                                                                                                        
                                                        442

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with GCYB1_HUMAN | Q02153 from UniProtKB/Swiss-Prot  Length:619

    Alignment length:197
                                   421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       
          GCYB1_HUMAN   412 VPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCLMSPENSDPQFHLEHRGPVSMKGKKEPMQVWFLSRKN 608
               SCOP domains d2wz1b_ B: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Guanylate_cyc-2wz1B01 B:412- 606                                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) Guanylate_cyc-2wz1B02 B:412- 606                                                                                                                                                                   -- Pfam domains (2)
         Sec.struct. author ...eeeeeeeeeeeee.hhhhhhh....-hhhhhhhhhhhhhhhhhhhhhh.......eee......eeeee.......hhhhhhhhhhhhhhhhhhhhee..ee..eeeeeeeeeeeeeee.....eeeeehhhhhhhhhhhhh.....eeeehhhhhhhh........eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------GUANYLATE_CYCLASE_2  PDB: B:421-554 UniProt: 421-554                                                                                  ------------------------------------------------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------GUANYLATE_CYCLASE_1     ------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wz1 B 412 VPAKRYDNVTILFSGIVGFNAFCSKHAS-EGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCLMSPENSDPQFHLEHRGPVSMKGKKEPMQVWFLSRKN 608
                                   421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       
                                                     439 |                                                                                                                                                                       
                                                       441

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ferredoxin-like (1795)

Superfamily: Nucleotide cyclase (51)

Family: automated matches (7)

Protein domain: automated matches (7)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2wz1a_	A:
1b	d2wz1b_	B:

(no "CATH Domain" information available for 2WZ1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Nucleot_cyclase (14)

Family: Guanylate_cyc (8)

Homo sapiens (Human) (1)

1a	Guanylate_cyc-2wz1B01	B:412-606
1b	Guanylate_cyc-2wz1B02	B:412-606

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GCYB1_HUMAN | Q02153)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0004016	adenylate cyclase activity	Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate.
	GO:0004383	guanylate cyclase activity	Catalysis of the reaction: GTP = 3',5'-cyclic GMP + diphosphate.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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:0016849	phosphorus-oxygen lyase activity	Catalysis of the cleavage of a phosphorus-oxygen bond by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	GO:0008015	blood circulation	The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
	GO:0006182	cGMP biosynthetic process	The chemical reactions and pathways resulting in the formation of cyclic GMP, guanosine 3',5'-phosphate.
	GO:0071732	cellular response to nitric oxide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
	GO:0009190	cyclic nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	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:0038060	nitric oxide-cGMP-mediated signaling pathway	Any intracellular signal transduction in which the signal is passed on within the cell by nitric oxide (NO) activating soluble guanylyl cyclase (sGC). Includes synthesis of nitric oxide, guanylyl cyclase activity, and downstream effectors that further transmit the signal within the cell following activation by cGMP.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0008074	guanylate cyclase complex, soluble	Complex that possesses guanylate cyclase activity and is not bound to a membrane.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Leu A:485 - Pro A:486	[ RasMol ]
		Leu B:485 - Pro B:486	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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