3GC6 - JenaLib

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Title :   STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM OF CD38: EVIDENCE FOR A CONFORMATIONALLY FLEXIBLE COVALENT ENZYME-SUBSTRATE COMPLEX.

Authors :   P. F. Egea, H. Muller-Steffner, R. M. Stroud, N. Oppenheimer, E. Kellen F. Schuber

Date :   21 Feb 09 (Deposition) - 02 Mar 10 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.51

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

Keywords :   Cd38, Cyclic Adp Ribose, Ecto-Adp-Ribosyl Cyclase, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. F. Egea, H. Muller-Steffner, I. Kuhn, C. Cakir-Kiefer, N. J. Oppenheimer, R. M. Stroud, E. Kellenberger, F. Schuber
Insights Into The Mechanism Of Bovine Cd38/Nad+Glycohydrolase From The X-Ray Structures Of Its Michaelis Complex And Covalently-Trapped Intermediates.
Plos One V. 7 34918 2012
PubMed-ID: 22529956 | Reference-DOI: 10.1371/JOURNAL.PONE.0034918

Molecule 1 - ECTO-NAD+ GLYCOHYDROLASE (CD38 MOLECULE)
	Chains	:	A, B
	EC Number	:	3.2.2.5
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Taxid	:	4922
	Gene	:	CD38
	Mutation	:	YES
	Organism Common	:	BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A (1x)	B (1x)
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:61 , THR A:65 , ARG B:71 , SER B:72 , HOH B:332	BINDING SITE FOR RESIDUE SO4 A 279
2	AC2	SOFTWARE	TYR A:36 , LEU A:39 , ARG A:131 , ARG A:133 , HOH A:486 , HOH A:579 , ASN B:268	BINDING SITE FOR RESIDUE SO4 A 280
3	AC3	SOFTWARE	LYS A:120 , SER A:212 , ILE A:213 , HOH A:311 , HOH A:511	BINDING SITE FOR RESIDUE SO4 A 281
4	AC4	SOFTWARE	LYS A:120 , THR A:121 , ASN A:201 , VAL A:233 , ASP A:235 , ARG A:271 , HOH A:323 , NAG A:502 , HOH A:554	BINDING SITE FOR RESIDUE NAG A 501
5	AC5	SOFTWARE	NAG A:501	BINDING SITE FOR RESIDUE NAG A 502
6	AC6	SOFTWARE	ARG A:259 , GLY B:69 , SER B:70 , ARG B:71 , ARG B:73	BINDING SITE FOR RESIDUE SO4 B 279
7	AC7	SOFTWARE	GLN A:76 , GLN B:76 , ARG B:79 , GLN B:80	BINDING SITE FOR RESIDUE SO4 B 280
8	AC8	SOFTWARE	LYS B:120 , THR B:121 , ASN B:201 , VAL B:233 , ASP B:235 , HOH B:357 , HOH B:373 , NAG B:502	BINDING SITE FOR RESIDUE NAG B 501
9	AC9	SOFTWARE	GLU B:123 , NAG B:501	BINDING SITE FOR RESIDUE NAG B 502

Asymmetric Unit

No.	Residues
1	A:59	-	A:75
2	A:92	-	A:172
3	A:112	-	A:193
4	A:152	-	A:165
5	A:244	-	A:265
6	B:59	-	B:75
7	B:92	-	B:172
8	B:112	-	B:193
9	B:152	-	B:165
10	B:244	-	B:265

(no "Cis Peptide Bond" information available for 3GC6)

(no "SAP(SNP)/Variant" information available for 3GC6)

(no "PROSITE Motif" information available for 3GC6)

(no "Exon" information available for 3GC6)

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:242
 aligned with Q9TTF5_BOVIN | Q9TTF5 from UniProtKB/TrEMBL  Length:278

    Alignment length:242
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275  
         Q9TTF5_BOVIN    36 YSGLNRWHGAGSTADFQKIIQERCDTYTQTIRPGSRSRNCQAIRQAFMSAFISKDPCKATKEDYNSLINLAPPTVPCGQQVFWSKTKELAHEYAKRRRLMTLEDTLLGYLADGLRWCGEPGSSDLNIWSCPDWRKDCRTNYLSVFWEVLSERFAESACNTVRVVLNGSLENAFDSMSIFGRVEAPNLRPQVELEAWLVHDTGKPPSDSCSGSSIRKLKSILDGRNVKFRCMDNLSRDQFLQR 277
               SCOP domains d3gc6a_ A: ADP ribosyl cyclase                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.......hhhhhhhhhhhh.........eeee.hhhhhhhhhhhhh..hhhhhhhhhhhh................ee.........hhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhh....eeeeeeee...........hhhhhhhhhhhhhh..eeeeeeeeehhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gc6 A  36 YSGLNRWHGAGSTADFQKIIQERCDTYTQTIRPGSRSRNCQAIRQAFMSAFISKDPCKATKEDYNSLINLAPPTVPCGQQVFWSKTKELAHEYAKRRRLMTLEDTLLGYLADGLRWCGEPGSSDLNIWSCPDWRKDCRTNYLSVFWEVLSERFAESACNTVRVVLNGSLENAFDSMSIFGRVQAPNLRPQVELEAWLVHDTGKPPSDSCSGSSIRKLKSILDGRNVKFRCMDNLSRDQFLQR 277
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275

Chain B from PDB  Type:PROTEIN  Length:237
 aligned with Q9TTF5_BOVIN | Q9TTF5 from UniProtKB/TrEMBL  Length:278

    Alignment length:237
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       
         Q9TTF5_BOVIN    39 LNRWHGAGSTADFQKIIQERCDTYTQTIRPGSRSRNCQAIRQAFMSAFISKDPCKATKEDYNSLINLAPPTVPCGQQVFWSKTKELAHEYAKRRRLMTLEDTLLGYLADGLRWCGEPGSSDLNIWSCPDWRKDCRTNYLSVFWEVLSERFAESACNTVRVVLNGSLENAFDSMSIFGRVEAPNLRPQVELEAWLVHDTGKPPSDSCSGSSIRKLKSILDGRNVKFRCMDNLSRDQFL 275
               SCOP domains d3gc6b_ B: ADP ribosyl cyclase                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.......hhhhhhhhhhhh.........eeee.hhhhhhhhhhhhh..hhhhhhhhhhhh................ee.........hhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhh....eeeeeeee...........hhhhhhhhhhhhhhh.eeeeeeeeehhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gc6 B  39 LNRWHGAGSTADFQKIIQERCDTYTQTIRPGSRSRNCQAIRQAFMSAFISKDPCKATKEDYNSLINLAPPTVPCGQQVFWSKTKELAHEYAKRRRLMTLEDTLLGYLADGLRWCGEPGSSDLNIWSCPDWRKDCRTNYLSVFWEVLSERFAESACNTVRVVLNGSLENAFDSMSIFGRVQAPNLRPQVELEAWLVHDTGKPPSDSCSGSSIRKLKSILDGRNVKFRCMDNLSRDQFL 275
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268

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(

)

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)

Cow (Bos taurus) [TaxId: 9913] (3)

1a	d3gc6a_	A:
1b	d3gc6b_	B:

(no "CATH Domain" information available for 3GC6)

(no "Pfam Domain" information available for 3GC6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9TTF5_BOVIN | Q9TTF5)

molecular function
	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.
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: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: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: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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	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.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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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Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (10, 10)

Cis Peptide Bonds (0, 0)

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