3N0Y - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ADENYLATE CYCLASE CLASS IV WITH ACTIVE SITE LIGAND APC

Authors :   D. T. Gallagher, P. T. Reddy

Date :   14 May 10 (Deposition) - 24 Nov 10 (Release) - 22 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Cyth Domain, Antiparallel Barrel, Substrate Analog Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. T. Gallagher, S. K. Kim, H. Robinson, P. T. Reddy
Active-Site Structure Of Class Iv Adenylyl Cyclase And Transphyletic Mechanism.
J. Mol. Biol. V. 405 787 2011
PubMed-ID: 21094652 | Reference-DOI: 10.1016/J.JMB.2010.11.026

Molecule 1 - ADENYLATE CYCLASE 2
	Chains	:	A, B
	EC Number	:	4.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CYAB, Y3011, YPO1178, YP_0959
	Mutation	:	YES
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Synonym	:	PUTATIVE ADENYLATE CYCLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	APC	2	Ligand/Ion	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2	MN	2	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:5 , GLU A:10 , GLU A:12 , LYS A:14 , ARG A:63 , LEU A:72 , LYS A:76 , CYS A:83 , ALA A:85 , ASN A:87 , LYS A:111 , ARG A:113 , GLU A:136 , SER A:172 , TYR A:173 , MN A:182 , HOH A:317 , HOH A:452	BINDING SITE FOR RESIDUE APC A 181
2	AC2	SOFTWARE	GLU A:12 , GLU A:136 , APC A:181	BINDING SITE FOR RESIDUE MN A 182
3	AC3	SOFTWARE	PHE B:5 , GLU B:10 , GLU B:12 , LYS B:14 , ASP B:43 , ARG B:63 , LEU B:72 , ILE B:74 , LYS B:76 , LYS B:111 , ARG B:113 , GLU B:136 , MET B:140 , SER B:172 , TYR B:173 , MN B:182 , HOH B:399 , HOH B:451	BINDING SITE FOR RESIDUE APC B 181
4	AC4	SOFTWARE	GLU B:12 , GLU B:136 , APC B:181	BINDING SITE FOR RESIDUE MN B 182

(no "SS Bond" information available for 3N0Y)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:66	-	Pro A:67
2	Gly A:77	-	Pro A:78
3	Asn B:66	-	Pro B:67
4	Gly B:77	-	Pro B:78

(no "SAP(SNP)/Variant" information available for 3N0Y)

(no "PROSITE Motif" information available for 3N0Y)

(no "Exon" information available for 3N0Y)

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:176
 aligned with Q7CH76_YERPE | Q7CH76 from UniProtKB/TrEMBL  Length:179

    Alignment length:176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      
         Q7CH76_YERPE     4 HFVGKYEVELKFRVMDLTTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLADQQISMVLREMNPSGIRLWIVKGPGAERCEASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTDDATELDKLKAECRDFANTFGLQVDQQEPRSYRQLLGF 179
               SCOP domains d3n0ya_ A: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhh..eeeeeeeeeeeeeee.....hhhhh.eeeeeeee....eeeeee......eeeee..hhhhhhhhhhhh..eeeeeeeeeeeeeee..eeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0y A   4 HFVGKYEVELKFRVMDLTTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLAKQQISMVLREMNPSGIRLWIVKGPGAERCEASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTDDATELDKLKAECRDFANTFGLQVDQQEPRSYRQLLGF 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with Q7CH76_YERPE | Q7CH76 from UniProtKB/TrEMBL  Length:179

    Alignment length:176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      
         Q7CH76_YERPE     4 HFVGKYEVELKFRVMDLTTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLADQQISMVLREMNPSGIRLWIVKGPGAERCEASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTDDATELDKLKAECRDFANTFGLQVDQQEPRSYRQLLGF 179
               SCOP domains d3n0yb_ B: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----CYTH-3n0yB01 B:8-179                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) ----CYTH-3n0yB02 B:8-179                                                                                                                                                         Pfam domains (2)
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhh..eeeeeeeeeeeeeeee....hhhhh.eeeeeeee....eeeeee......eeeee..hhhhhhhhhhhh.eeeeeeeeeeeeeeee..eeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhh...hhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0y B   4 HFVGKYEVELKFRVMDLTTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLAKQQISMVLREMNPSGIRLWIVKGPGAERCEASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTDDATELDKLKAECRDFANTFGLQVDQQEPRSYRQLLGF 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

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: CYTH-like phosphatases (16)

Superfamily: CYTH-like phosphatases (16)

Family: automated matches (5)

Protein domain: automated matches (5)

Yersinia pestis [TaxId: 632] (3)

1a	d3n0ya_	A:
1b	d3n0yb_	B:

(no "CATH Domain" information available for 3N0Y)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CYTH (6)

Family: CYTH (4)

Yersinia pestis (3)

1a	CYTH-3n0yB01	B:8-179
1b	CYTH-3n0yB02	B:8-179

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q7CH76_YERPE | Q7CH76)

molecular function
	GO:0004016	adenylate cyclase activity	Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate.
	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.
biological process
	GO:0006171	cAMP biosynthetic process	The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asn A:66 - Pro A:67	[ RasMol ]
		Asn B:66 - Pro B:67	[ RasMol ]
		Gly A:77 - Pro A:78	[ RasMol ]
		Gly B:77 - Pro B:78	[ RasMol ]

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	3n0y
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	4.6.1.1
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UniProtKB/TrEMBL
	Q7CH76_YERPE \| Q7CH76	:	2fjt 3n0z 3n10

2fjt	WILDTYPE UNLIGANDED ENZYME
3n0z	ENZYME W 3AT LIGAND
3n10

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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