3G5I - JenaLib

Title :   CRYSTAL STRUCTURE OF THE E.COLI RIHA PYRIMIDINE NUCLEOSIDASE BOUND TO A IMINORIBITOL-BASED INHIBITOR

Authors :   G. Garau, L. Muzzolini, P. Tornaghi, M. Degano

Date :   05 Feb 09 (Deposition) - 09 Feb 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Open (Alpha, Beta) Structure, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Garau, L. Muzzolini, P. Tornaghi, M. Degano
Crystal Structure Of The Riha Nucleoside Hydrolase Bound To A Competitive Inhibitor
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - PYRIMIDINE-SPECIFIC RIBONUCLEOSIDE HYDROLASE RIHA
	Chains	:	A, B, C, D
	EC Number	:	3.2.2.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YBEK
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	RIHA/YBEK PYRIMIDINE NUCLEOSIDE HYDROLASE, CYTIDINE/URIDINE- SPECIFIC HYDROLASE

Structural Features

Chains, Units

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 9)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CA	4	Ligand/Ion	CALCIUM ION
3	DNB	4	Ligand/Ion	(2S,3S,4R,5R)-2-(3,4-DIAMINOPHENYL)-5-(HYDROXYMETHYL)PYRROLIDINE-3,4-DIOL

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:100 , CYS A:102 , LEU A:107 , LYS A:110 , GLU C:114	BINDING SITE FOR RESIDUE BME A 1102
2	AC2	SOFTWARE	ASP A:10 , ASP A:15 , ASN A:39 , THR A:124 , ASP A:241 , HOH A:312 , DNB A:502	BINDING SITE FOR RESIDUE CA A 501
3	AC3	SOFTWARE	ASP A:14 , ASP A:15 , ASN A:39 , VAL A:81 , HIS A:82 , THR A:124 , MET A:150 , ASN A:158 , GLU A:164 , ASN A:166 , ASP A:241 , HOH A:312 , CA A:501	BINDING SITE FOR RESIDUE DNB A 502
4	AC4	SOFTWARE	ASP B:10 , ASP B:15 , ASN B:39 , THR B:124 , ASP B:241 , HOH B:455 , DNB B:502	BINDING SITE FOR RESIDUE CA B 501
5	AC5	SOFTWARE	ASP B:14 , ASP B:15 , ASN B:39 , THR B:124 , MET B:150 , ASN B:158 , TRP B:159 , GLU B:164 , ASN B:166 , ASP B:241 , HOH B:455 , CA B:501	BINDING SITE FOR RESIDUE DNB B 502
6	AC6	SOFTWARE	ASP C:10 , ASP C:15 , ASN C:39 , THR C:124 , ASP C:241 , DNB C:502 , HOH C:573	BINDING SITE FOR RESIDUE CA C 501
7	AC7	SOFTWARE	ASP C:14 , ASP C:15 , ASN C:39 , THR C:124 , MET C:150 , ASN C:158 , GLU C:164 , PHE C:165 , ASN C:166 , ASP C:241 , CA C:501 , HOH C:573	BINDING SITE FOR RESIDUE DNB C 502
8	AC8	SOFTWARE	ASP D:10 , ASP D:15 , ASN D:39 , THR D:124 , ASP D:241 , HOH D:390 , DNB D:502	BINDING SITE FOR RESIDUE CA D 501
9	AC9	SOFTWARE	ASP D:14 , ASP D:15 , ASN D:39 , THR D:124 , MET D:150 , ASN D:158 , TRP D:159 , GLU D:164 , ASN D:166 , ASP D:241 , HOH D:390 , CA D:501	BINDING SITE FOR RESIDUE DNB D 502

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IUNH	PS01247	Inosine-uridine preferring nucleoside hydrolase family signature.	RIHA_ECOLI	8-18	4	A:8-18 B:8-18 C:8-18 D:8-18

Exons (0, 0)

Sequences/Alignments

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:305
 aligned with RIHA_ECOLI | P41409 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
           RIHA_ECOLI     2 ALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKDEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA 311
               SCOP domains d3g5ia_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3g5iA00 A:2-311 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhh......eee.....................................hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeeeee.............hhhhhhhhhhhhhhhh....eeeehhhhhh..eehhhhhhhhhhh.hhhhhhhhhhhhhh.-----.......ee..hhhhhhhhhh...eeeeee.eee..........eee...........eeeeeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------IUNH       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5i A   2 ALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFL-----EKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA 311
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  |    231       241       251       261       271       281       291       301       311
                                                                                                                                                                                                                                                        224   230

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with RIHA_ECOLI | P41409 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 
           RIHA_ECOLI     1 MALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKDEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA 311
               SCOP domains d3g5ib_ B: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3g5iB00 B:1-311 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhh......eee..........----------.................hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeeeee.............hhhhhhhhhhhhhhhhh...eeeehhhhhh..eehhhhhhhhhhh.hhhhhhhhhhhhhhh------......ee..hhhhhhhhhh...eeeeee.eee..........eee...........eeeeeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------IUNH       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5i B   1 SALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMREL----------GLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFL------KWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA 311
                                    10        20        30        40        50        60        70    |    -     |  90       100       110       120       130       140       150       160       170       180       190       200       210       220   |     -|      240       250       260       270       280       290       300       310 
                                                                                                     75         86                                                                                                                                       224    231

Chain C from PDB  Type:PROTEIN  Length:293
 aligned with RIHA_ECOLI | P41409 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
           RIHA_ECOLI     2 ALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKDEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA 311
               SCOP domains d3g5ic_ C: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3g5iC00 C:2-311 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhh......eee..........----------.................hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeeeee.............hhhhhhhhhhhhhhhhh...eeeehhhhhh..eehhhhhhhhhhh.hhhhhhhhhhhhh-------.......ee..hhhhhhhhhh...eeeeee.eee..........eee...........eeeeeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------IUNH       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5i C   2 ALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMREL----------GLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDF-------EKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA 311
                                    11        21        31        41        51        61        71   |     -    |   91       101       111       121       131       141       151       161       171       181       191       201       211       221|      231       241       251       261       271       281       291       301       311
                                                                                                    75         86                                                                                                                                     222     230

Chain D from PDB  Type:PROTEIN  Length:304
 aligned with RIHA_ECOLI | P41409 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:312
                             1                                                                                                                                                                                                                                                                                                                      
                             |       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       259       269       279       289       299       309  
           RIHA_ECOLI     - -MALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKDEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA 311
               SCOP domains d3g5id_ D: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3g5iD00 D:0-311 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhhh......eee...........--------..................hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh.eeeeeee.............hhhhhhhhhhhhhhhh....eeeehhhhhh..eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........ee..hhhhhhhhhh...eeeeee.eee..........eee...........eeeeeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------IUNH       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3g5i D   0 GSALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELI--------SGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKDEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA 311
                                     9        19        29        39        49        59        69      |  -     |  89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309  
                                                                                                       76       85

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	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 '\|'

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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