2HCT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ACIDIC RESIDUES AT THE ACTIVE SITES OF CD38 AND ADP-RIBOSYL CYCLASE DETERMINE NAAPD SYNTHESIS AND HYDROLYSIS ACTIVITIES

Authors :   Q. Liu, I. A. Kriksunov, Q. Hao, R. Graeff, H. C. Lee

Date :   18 Jun 06 (Deposition) - 22 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Beta Sheets, Alpha Bundle, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Graeff, Q. Liu, I. A. Kriksunov, Q. Hao, H. C. Lee
Acidic Residues At The Active Sites Of Cd38 And Adp-Ribosyl Cyclase Determine Nicotinic Acid Adenine Dinucleotide Phosphate (Naadp) Synthesis And Hydrolysis Activities.
J. Biol. Chem. V. 281 28951 2006
PubMed-ID: 16861223 | Reference-DOI: 10.1074/JBC.M604370200

Molecule 1 - ADP-RIBOSYL CYCLASE 1
	Chains	:	A, B
	EC Number	:	3.2.2.5
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZAA
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Fragment	:	ENZYMATIC DOMAIN, RESIDUES 45-300
	Gene	:	CD38
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYCLIC ADP-RIBOSE HYDROLASE 1, CADPR HYDROLASE 1, LYMPHOCYTE DIFFERENTIATION ANTIGEN CD38, T10, ACUTE LYMPHOBLASTIC LEUKEMIA CELLS ANTIGEN CD38

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	NMN	2	Ligand/Ion	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NMN	1	Ligand/Ion	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NMN	1	Ligand/Ion	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:125 , SER A:126 , ARG A:127 , LEU A:145 , GLU A:146 , ASP A:155 , ASP A:156 , TRP A:189 , SER A:193 , SER A:220 , THR A:221 , PHE A:222 , HOH A:404	BINDING SITE FOR RESIDUE NMN A 301
2	AC2	SOFTWARE	TRP B:125 , SER B:126 , ARG B:127 , LYS B:129 , LEU B:145 , GLU B:146 , ASP B:155 , ASP B:156 , TRP B:189 , SER B:193 , SER B:220 , THR B:221 , PHE B:222 , HOH B:415	BINDING SITE FOR RESIDUE NMN B 302

Asymmetric Unit

No.	Residues
1	A:67	-	A:82
2	A:99	-	A:180
3	A:119	-	A:201
4	A:160	-	A:173
5	A:254	-	A:275
6	A:287	-	A:296
7	B:67	-	B:82
8	B:99	-	B:180
9	B:119	-	B:201
10	B:160	-	B:173
11	B:254	-	B:275
12	B:287	-	B:296

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_001323	R	140	W	CD38_HUMAN	Polymorphism	1800561	A/B	R	140	W

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_001323	R	140	W	CD38_HUMAN	Polymorphism	1800561	A	R	140	W

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_001323	R	140	W	CD38_HUMAN	Polymorphism	1800561	B	R	140	W

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

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

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000226279	1b	ENSE00001131145	chr4:15779901-15780270	370	CD38_HUMAN	1-78	78	2	A:45-78 B:45-78	34 34
1.2a	ENST00000226279	2a	ENSE00000705354	chr4:15818134-15818263	130	CD38_HUMAN	78-121	44	2	A:78-121 B:78-121	44 44
1.3b	ENST00000226279	3b	ENSE00000705352	chr4:15826504-15826639	136	CD38_HUMAN	122-167	46	2	A:122-167 B:122-167	46 46
1.4	ENST00000226279	4	ENSE00000404201	chr4:15835840-15835925	86	CD38_HUMAN	167-195	29	2	A:167-195 B:167-195	29 29
1.5	ENST00000226279	5	ENSE00000705349	chr4:15839715-15839788	74	CD38_HUMAN	196-220	25	2	A:196-220 B:196-220	25 25
1.6	ENST00000226279	6	ENSE00000705347	chr4:15841649-15841741	93	CD38_HUMAN	220-251	32	2	A:220-251 B:220-251	32 32
1.7b	ENST00000226279	7b	ENSE00000404204	chr4:15842075-15842161	87	CD38_HUMAN	251-280	30	2	A:251-280 B:251-280	30 30
1.8b	ENST00000226279	8b	ENSE00001131136	chr4:15850162-15851069	908	CD38_HUMAN	280-300	21	2	A:280-296 B:280-296	17 17

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:252
 aligned with CD38_HUMAN | P28907 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:252
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
           CD38_HUMAN    45 RWRQQWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCNITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFNTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLNGSRSKIFDKNSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSC 296
               SCOP domains d2hcta_ A: ADP ribosyl cyclase                                                                                                                                                                                                                               SCOP domains
               CATH domains 2hctA01 A:45-116,A:144-199 ADP Ribosyl Cyclase; Chain A, domain 1       ---------------------------2hctA01 A:45-116,A:144-199                              ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhh.eeee.hhhhhhhhhhhh....hhhhhhhhhhhh...........................hhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhhhhhhhh....eeeeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------W------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:45-78           -------------------------------------------Exon 1.3b  PDB: A:122-167 UniProt: 122-167    ----------------------------Exon 1.5  PDB: A:196-220 ------------------------------Exon 1.7b  PDB: A:251-280     ---------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.2a  PDB: A:78-121 UniProt: 78-121    ---------------------------------------------Exon 1.4  PDB: A:167-195     ------------------------Exon 1.6  PDB: A:220-251        ----------------------------Exon 1.8b         Transcript 1 (2)
                 2hct A  45 RWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVGVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSC 296
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with CD38_HUMAN | P28907 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:252
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
           CD38_HUMAN    45 RWRQQWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCNITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFNTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLNGSRSKIFDKNSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSC 296
               SCOP domains d2hctb_ B: ADP ribosyl cyclase                                                                                                                                                                                                                               SCOP domains
               CATH domains 2hctB01 B:45-116,B:144-199 ADP Ribosyl Cyclase; Chain A, domain 1       ---------------------------2hctB01 B:45-116,B:144-199                              ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhh.........eeee.hhhhhhhhhhhh....hhhhhhhhhhhh................ee.........hhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhhh.........eeeeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------W------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: B:45-78           -------------------------------------------Exon 1.3b  PDB: B:122-167 UniProt: 122-167    ----------------------------Exon 1.5  PDB: B:196-220 ------------------------------Exon 1.7b  PDB: B:251-280     ---------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.2a  PDB: B:78-121 UniProt: 78-121    ---------------------------------------------Exon 1.4  PDB: B:167-195     ------------------------Exon 1.6  PDB: B:220-251        ----------------------------Exon 1.8b         Transcript 1 (2)
                 2hct B  45 RWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLDGSRSKIFDKDSTFGSVGVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSC 296
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294

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(

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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: ADP ribosyl cyclase (42)

Human (Homo sapiens) [TaxId: 9606] (33)

1a	d2hcta_	A:
1b	d2hctb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: ADP Ribosyl Cyclase; Chain A, domain 1 (29)

Homologous Superfamily: ADP Ribosyl Cyclase; Chain A, domain 1 (29)

Human (Homo sapiens) (20)

1a	2hctA01	A:45-116,A:144-199
1b	2hctB01	B:45-116,B:144-199

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CD38_HUMAN | P28907)

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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	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: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:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0007565	female pregnancy	The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
	GO:0060292	long term synaptic depression	A process that modulates synaptic plasticity such that synapses are changed resulting in the decrease in the rate, or frequency of synaptic transmission at the synapse.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0045779	negative regulation of bone resorption	Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0030890	positive regulation of B cell proliferation	Any process that activates or increases the rate or extent of B cell proliferation.
	GO:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0007204	positive regulation of cytosolic calcium ion concentration	Any process that increases the concentration of calcium ions in the cytosol.
	GO:0032024	positive regulation of insulin secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0045907	positive regulation of vasoconstriction	Any process that activates or increases the frequency, rate or extent of vasoconstriction.
	GO:0034097	response to cytokine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0032355	response to estradiol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0009725	response to hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
	GO:0033194	response to hydroperoxide	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydroperoxide stimulus. Hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH.
	GO:0001666	response to hypoxia	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0070555	response to interleukin-1	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
	GO:0032570	response to progesterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus.
	GO:0032526	response to retinoic acid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
	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:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the 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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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.

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Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (12, 12)

Cis Peptide Bonds (0, 0)

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