1S2I - JenaLib

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Title :   PURINE 2'DEOXYRIBOSYLTRANSFERASE + BROMOPURINE

Authors :   R. Anand, P. A. Kaminski, S. E. Ealick

Date :   08 Jan 04 (Deposition) - 30 Mar 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.24

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

Keywords :   Ptd, Bropmpurine, Brpur, 2'-Purine Deoxyribosyltansferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Anand, P. A. Kaminski, S. E. Ealick
Structures Of Purine 2'-Deoxyribosyltransferase, Substrate Complexes, And The Ribosylated Enzyme Intermediate At 2. 0 A Resolution.
Biochemistry V. 43 2384 2004
PubMed-ID: 14992575 | Reference-DOI: 10.1021/BI035723K

Molecule 1 - PURINE TRANS DEOXYRIBOSYLASE
	Chains	:	A, B, C
	EC Number	:	2.4.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	LACTOBACILLUS HELVETICUS
	Organism Taxid	:	1587

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	BP1	3	Ligand/Ion	6-BROMO-7H-PURINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	BP1	6	Ligand/Ion	6-BROMO-7H-PURINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:44 , PHE A:45 , THR A:71 , ASP A:75 , TYR C:167	BINDING SITE FOR RESIDUE BP1 A 1245
2	AC2	SOFTWARE	TYR B:17 , PRO B:44 , PHE B:45 , THR B:71 , ASP B:75 , TYR B:167 , HOH B:2254	BINDING SITE FOR RESIDUE BP1 B 2245
3	AC3	SOFTWARE	TYR A:167 , PRO C:44 , PHE C:45 , THR C:71 , ASP C:75 , HOH C:3257	BINDING SITE FOR RESIDUE BP1 C 3245

(no "SS Bond" information available for 1S2I)

(no "Cis Peptide Bond" information available for 1S2I)

(no "SAP(SNP)/Variant" information available for 1S2I)

(no "PROSITE Motif" information available for 1S2I)

(no "Exon" information available for 1S2I)

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:165
 aligned with Q8RLY5_LACHE | Q8RLY5 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8RLY5_LACHE     1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
               SCOP domains d1s2ia_ A: Purine transdeoxyribosylase                                                                                                                                  SCOP domains
               CATH domains 1s2iA00 A:1-167  [code=3.40.50.1810, no name d efined]                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhhh...eeeee....-........-.......hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eehhhhhhhh.ee.....hhhhhhh..............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2i A   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFD-GFTDPDEK-PEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40     | |50    | | 60        70        80        90       100       110       120       130       140       150       160       
                                                                        46 |     55 |                                                                                                              
                                                                          48       57

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with Q8RLY5_LACHE | Q8RLY5 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8RLY5_LACHE     1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
               SCOP domains d1s2ib_ B: Purine transdeoxyribosylase                                                                                                                                  SCOP domains
               CATH domains 1s2iB00 B:1-167  [code=3.40.50.1810, no name defined]                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhhhh..eeeee.....................hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eeehhhhhhh.ee.hhhhhhhhhhh..............eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2i B   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:167
 aligned with Q8RLY5_LACHE | Q8RLY5 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8RLY5_LACHE     1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
               SCOP domains d1s2ic_ C: Purine transdeoxyribosylase                                                                                                                                  SCOP domains
               CATH domains 1s2iC00 C:1-167  [code=3.40.50.1810, no name defined]                                                                                                                   CATH domains
           Pfam domains (1) ---------Nuc_deoxyrib_tr-1s2iC01 C:10-130                                                                                         ------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------Nuc_deoxyrib_tr-1s2iC02 C:10-130                                                                                         ------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------Nuc_deoxyrib_tr-1s2iC03 C:10-130                                                                                         ------------------------------------- Pfam domains (3)
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eeehhhhhhh.ee.hhhhhhhhhhh..............eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2i C   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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: N-deoxyribosyltransferase (12)

Protein domain: Purine transdeoxyribosylase (5)

Lactobacillus helveticus [TaxId: 1587] (5)

1a	d1s2ia_	A:
1b	d1s2ib_	B:
1c	d1s2ic_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1810, no name defined] (8)

Lactobacillus helveticus. Organism_taxid: 1587. (5)

1a	1s2iA00	A:1-167
1b	1s2iB00	B:1-167
1c	1s2iC00	C:1-167

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Nribosyltransf (19)

Family: Nuc_deoxyrib_tr (4)

Lactobacillus helveticus (Lactobacillus suntoryeus) (4)

1a	Nuc_deoxyrib_tr-1s2iC01	C:10-130
1b	Nuc_deoxyrib_tr-1s2iC02	C:10-130
1c	Nuc_deoxyrib_tr-1s2iC03	C:10-130

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q8RLY5_LACHE | Q8RLY5)

molecular function
	GO:0070694	deoxyribonucleoside 5'-monophosphate N-glycosidase activity	Catalysis of the reaction: a deoxyribonucleoside 5'-monophosphate + H2O = deoxyribose 5-monophosphate + a purine or pyrimidine base.
	GO:0050144	nucleoside deoxyribosyltransferase activity	Catalysis of the reaction: 2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1.
	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.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0009159	deoxyribonucleoside monophosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.

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Biological Unit
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1f8y	STRUCTURE OF 2'-DEOXYRIBOSYLTRANSFERASE(NTD)
1s2d	PURINE 2'-DEOXYRIBOSYL COMPLEX WITH ARABINOSIDE: RIBOSYLATED INTERMEDIATE (ARAA)
1s2g	PURINE 2'DEOXYRIBOSYLTRANSFERASE + 2'-DEOXYADENOSINE
1s2l	PURINE 2'DEOXYRIBOSYLTRANSFERASE NATIVE STRUCTURE
1s3f	PURINE 2'-DEOXYRIBOSYLTRANSFERASE + SELENOINOSINE

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