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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF APLYSIA CYCLASE COMPLEXED WITH SUBSTRATE NGD AND PRODUCT CGDPR

Authors :   M. Kotaka, R. Graeff, L. H. Zhang, H. C. Lee, Q. Hao

Date :   02 Aug 11 (Deposition) - 30 Nov 11 (Release) - 25 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

Reference :   M. Kotaka, R. Graeff, Z. Chen, L. H. Zhang, H. C. Lee, Q. Hao
Structural Studies Of Intermediates Along The Cyclization Pathway Of Aplysia Adp-Ribosyl Cyclase.
J. Mol. Biol. V. 415 514 2012
PubMed-ID: 22138343 | Reference-DOI: 10.1016/J.JMB.2011.11.022

Molecule 1 - ADP-RIBOSYL CYCLASE
	Chains	:	A, B
	EC Number	:	3.2.2.5
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZALPHAA
	Expression System Strain	:	X-33
	Expression System Taxid	:	4922
	Organism Common	:	CALIFORNIA SEA HARE
	Organism Scientific	:	APLYSIA CALIFORNICA
	Organism Taxid	:	6500
	Synonym	:	ADRC, NAD GLYCOHYDROLASE, NAD(+) NUCLEOSIDASE, NADASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CGR	1	Ligand/Ion	CYCLIC GUANOSINE DIPHOSPHATE-RIBOSE
2	NGD	1	Ligand/Ion	3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHO(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]PYRIDINIUM

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:76 , TRP A:77 , SER A:78 , GLY A:79 , LEU A:97 , GLU A:98 , ASN A:107 , TRP A:140 , SER A:144 , ARG A:170 , SER A:173 , PHE A:174 , PHE A:175 , GLU A:179 , HOH A:3135 , HOH A:3156 , HOH A:3172 , HOH A:3193 , HOH A:3241	BINDING SITE FOR RESIDUE CGR A2458
2	AC2	SOFTWARE	PHE B:76 , TRP B:77 , SER B:78 , GLY B:79 , LEU B:97 , GLU B:98 , ASN B:107 , PHE B:128 , ARG B:136 , TRP B:140 , SER B:144 , ARG B:170 , SER B:173 , PHE B:174 , PHE B:175 , GLU B:179 , HOH B:6101 , HOH B:6120 , HOH B:6140 , HOH B:6162 , HOH B:6163 , HOH B:6209 , HOH B:6210 , HOH B:6211	BINDING SITE FOR RESIDUE NGD B5573

Asymmetric/Biological Unit

No.	Residues
1	A:15	-	A:34
2	A:51	-	A:131
3	A:112	-	A:125
4	A:206	-	A:227
5	A:239	-	A:248
6	B:15	-	B:34
7	B:51	-	B:131
8	B:112	-	B:125
9	B:206	-	B:227
10	B:239	-	B:248

Asymmetric/Biological Unit

No.	Residues
1	Asn A:117	-	Pro A:118
2	Asn B:117	-	Pro B:118

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

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

(no "Exon" information available for 3ZWN)

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:253
 aligned with NADA_APLCA | P29241 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:253
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   
           NADA_APLCA    23 EAIVPTRELENVFLGRCKDYEITRYLDILPRVRSDCSALWKDFFKAFSFKNPCDLDLGSYKDFFTSAQQQLPKNKVMFWSGVYDEAHDYANTGRKYITLEDTLPGYMLNSLVWCGQRANPGFNEKVCPDFKTCPVQARESFWGMASSSYAHSAEGEVTYMVDGSNPKVPAYRPDSFFGKYELPNLTNKVTRVKVIVLHRLGEKIIEKCGAGSLLDLEKLVKAKHFAFDCVENPRAVLFLLCSDNPNARECRLA 275
               SCOP domains d3zwna_ A: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..hhhhh....hhhhhhhhh.......eeeee.hhhhhhhhhh......hhhhhhhhhhhh.................ee.hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee............hhhhhhhhhhh...eeeeeeeee............hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zwn A  -1 AAIVPTRELENVFLGRCKDYEITRYLDILPRVRSDCSALWKDFFKAFSFKNPCDLDLGSYKDFFTSAQQQLPKNKVMFWSGVYDEAHDYANTGRKYITLEDTLPGYMLNSLVWCGQRANPGFNEKVCPDFKTCPVQARESFWGMASSSYAHSAEGEVTYMVDGSNPKVPAYRPDSFFGKYELPNLTNKVTRVKVIVLHRLGEKIIEKCGAGSLLDLEKLVKAKHFAFDCVENPRAVLFLLCSDNPNARECRLA 251
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with NADA_APLCA | P29241 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:252
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273  
           NADA_APLCA    24 AIVPTRELENVFLGRCKDYEITRYLDILPRVRSDCSALWKDFFKAFSFKNPCDLDLGSYKDFFTSAQQQLPKNKVMFWSGVYDEAHDYANTGRKYITLEDTLPGYMLNSLVWCGQRANPGFNEKVCPDFKTCPVQARESFWGMASSSYAHSAEGEVTYMVDGSNPKVPAYRPDSFFGKYELPNLTNKVTRVKVIVLHRLGEKIIEKCGAGSLLDLEKLVKAKHFAFDCVENPRAVLFLLCSDNPNARECRLA 275
               SCOP domains d3zwnb_ B: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh...........hhhhhhhhh.......eeeee.hhhhhhhhhh......hhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhh.eeeeeeee............hhhhhhhhhhh...eeeeeeeee............hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zwn B   0 AIVPTRELENVFLGRCKDYEITRYLDILPRVRSDCSALWKDFFKAFSFKNPCDLDLGSYKDFFTSAQQQLPKNKVMFWSGVYDEAHDYANTGRKYITLEDTLPGYMLNSLVWCGQRANPGFNEKVCPDFKTCPVQARESFWGMASSSYAHSAEGEVTYMVDGSNPKVPAYRPDSFFGKYELPNLTNKVTRVKVIVLHRLGEKIIEKCGAGSLLDLEKLVKAKHFAFDCVENPRAVLFLLCSDNPNARECRLA 251
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

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) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: N-(deoxy)ribosyltransferase-like (76)

Family: ADP ribosyl cyclase-like (60)

Protein domain: automated matches (12)

California sea hare (Aplysia californica) [TaxId: 6500] (12)

1a	d3zwna_	A:
1b	d3zwnb_	B:

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

(no "Pfam Domain" information available for 3ZWN)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NADA_APLCA | P29241)

molecular function
	GO:0050135	NAD(P)+ nucleosidase activity	Catalysis of the reaction: NAD(P)+ + H2O = ADP-ribose(P) + nicotinamide.
	GO:0003953	NAD+ nucleosidase activity	Catalysis of the reaction: NAD+ + H2O = nicotinamide + ADP-ribose.
	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:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0007338	single fertilization	The union of male and female gametes to form a zygote.
cellular component
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:117 - Pro A:118	[ RasMol ]
		Asn B:117 - Pro B:118	[ RasMol ]

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	3zwn
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	3.2.2.5
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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1lbe	APLYSIA ADP RIBOSYL CYCLASE
1r0s	CRYSTAL STRUCTURE OF ADP-RIBOSYL CYCLASE GLU179ALA MUTANT
1r12	NATIVE APLYSIA ADP RIBOSYL CYCLASE
1r15	APLYSIA ADP RIBOSYL CYCLASE WITH BOUND NICOTINAMIDE AND R5P
1r16	APLYSIA ADP RIBOSYL CYCLASE WITH BOUND PYRIDYLCARBINOL ANDR5P

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (10, 10)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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