2MAS - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PURINE NUCLEOSIDE HYDROLASE WITH A TRANSITION STATE INHIBITOR

Authors :   M. Degano, V. L. Schramm, J. C. Sacchettini

Date :   17 Oct 96 (Deposition) - 12 Aug 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Purine Nucleoside Hydrolase, Inosine, Uridine, Iu-Nh, Hydrolase, Purine Nucleosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Degano, S. C. Almo, J. C. Sacchettini, V. L. Schramm
Trypanosomal Nucleoside Hydrolase. A Novel Mechanism From The Structure With A Transition-State Inhibitor.
Biochemistry V. 37 6277 1998
PubMed-ID: 9572842 | Reference-DOI: 10.1021/BI973012E
(for further references see the PDB file header)

Molecule 1 - INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
	Chains	:	A, B, C, D
	EC Number	:	3.2.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	IU-NH FROM C. FASCICULATA
	Expression System Plasmid	:	PET3D-IUNH
	Expression System Taxid	:	562
	Gene	:	IU-NH FROM C. FASCICULATA
	Mutation	:	YES
	Organism Scientific	:	CRITHIDIA FASCICULATA
	Organism Taxid	:	5656
	Synonym	:	PURINE NUCLEOSIDE HYDROLASE, INOSINE-URIDINE NUCLEOSIDASE, IU-NH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	PIR	4	Ligand/Ion	2-(4-AMINO-PHENYL)-5-HYDROXYMETHYL-PYRROLIDINE-3,4-DIOL

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:10 , ASP A:15 , ASN A:39 , THR A:126 , ASP A:242 , PIR A:400 , HOH A:436	BINDING SITE FOR RESIDUE CA A 316
02	AC2	SOFTWARE	ASP B:10 , ASP B:15 , ASN B:39 , THR B:126 , ASP B:242 , PIR B:400 , HOH B:428	BINDING SITE FOR RESIDUE CA B 316
03	AC3	SOFTWARE	ASP C:10 , ASP C:15 , ASN C:39 , THR C:126 , ASP C:242 , PIR C:400 , HOH C:451	BINDING SITE FOR RESIDUE CA C 316
04	AC4	SOFTWARE	ASP D:10 , ASP D:15 , ASN D:39 , THR D:126 , ASP D:242 , PIR D:400 , HOH D:441	BINDING SITE FOR RESIDUE CA D 316
05	AC5	SOFTWARE	ASP A:14 , ASP A:15 , ASN A:39 , ILE A:81 , HIS A:82 , THR A:126 , MET A:152 , ASN A:160 , GLU A:166 , ASN A:168 , ARG A:233 , ASP A:242 , CA A:316 , HOH A:436	BINDING SITE FOR RESIDUE PIR A 400
06	AC6	SOFTWARE	ASP B:14 , ASP B:15 , ASN B:39 , ILE B:81 , HIS B:82 , THR B:126 , MET B:152 , ASN B:160 , GLU B:166 , ASN B:168 , ARG B:233 , ASP B:242 , CA B:316 , HOH B:428	BINDING SITE FOR RESIDUE PIR B 400
07	AC7	SOFTWARE	ASP C:14 , ASP C:15 , ASN C:39 , ILE C:81 , HIS C:82 , THR C:126 , MET C:152 , ASN C:160 , GLU C:166 , ASN C:168 , ASP C:242 , CA C:316 , HOH C:451	BINDING SITE FOR RESIDUE PIR C 400
08	AC8	SOFTWARE	ASP D:14 , ASP D:15 , ASN D:39 , ILE D:81 , THR D:126 , MET D:152 , ASN D:160 , GLU D:166 , ASN D:168 , ARG D:233 , ASP D:242 , CA D:316	BINDING SITE FOR RESIDUE PIR D 400
09	S1	UNKNOWN	ASP A:10 , ASP A:15 , ASP A:242 , HIS A:241 , HIS A:82	DESCRIPTION NOT PROVIDED
10	S2	UNKNOWN	ASP B:10 , ASP B:15 , ASP B:242 , HIS B:241 , HIS B:82	DESCRIPTION NOT PROVIDED
11	S3	UNKNOWN	ASP C:10 , ASP C:15 , ASP C:242 , HIS C:241 , HIS C:82	DESCRIPTION NOT PROVIDED
12	S4	UNKNOWN	ASP D:10 , ASP D:15 , ASP D:242 , HIS D:241 , HIS D:82	DESCRIPTION NOT PROVIDED

(no "SS Bond" information available for 2MAS)

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

(no "SAP(SNP)/Variant" information available for 2MAS)

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.	IUNH_CRIFA	8-18	4	A:8-18 B:8-18 C:8-18 D:8-18

(no "Exon" information available for 2MAS)

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
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Chain A from PDB  Type:PROTEIN  Length:313
 aligned with IUNH_CRIFA | Q27546 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:313
                                    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   
           IUNH_CRIFA     2 PKKIILDCDPGLDDAVAILLAHGNPEIELLAITTVVGNQTLAKVTRNAQLVADIAGITGVPIAAGCDKPLVRKIMTAGHIHGESGMGTVAYPAEFKNKVDERHAVNLIIDLVMSHEPKTITLVPTGGLTNIAMAARLEPRIVDRVKEVVLMGGGYHEGNATSVAEFNIIIDPEAAHIVFNESWQVTMVGLDLTHQALATPPILQRVKEVDTNPARFMLEIMDYYTKIYQSNRYMAAAAVHDPCAVAYVIDPSVMTTERVPVDIELTGKLTLGMTVADFRNPRPEHCHTQVAVKLDFEKFWGLVLDALERIGDP 314
               SCOP domains d2masa_ A: Inosine-uridine nucleoside N-ribohydrolase, IU-NH                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2masA00 A:2-314 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhh......eeee.............hhhh......................hhhhhhhhhhh.....eeeee....hhhhhhhhh.hhhhhh...eeee..............hhhhhhhhhhhhhhh....eeee.hhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.hhh..eee.eeee..........eeee..........eeee....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------IUNH       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mas A   2 AKKIILDCDPGLDDAVAILLAHGNPEIELLAITTVVGNQTLAKVTRNAQLVADIAGITGVPIAAGCDKPLVRKIMTAGHIHGESGMGTVAYPAEFKNKVDERHAVNLIIDLVMSHEPKTITLVPTGGLTNIAMAARLEPRIVDRVKEVVLMGGGYHEGNATSVAEFNIIIDPEAAHIVFNESWQVTMVGLDLTHQALATPPILQRVKEVDTNPARFMLEIMDYYTKIYQSNRYMAAAAVHDPCAVAYVIDPSVMTTERVPVDIELTGKLTLGMTVADFRNPRPEHCHTQVAVKLDFEKFWGLVLDALERIGDP 314
                                    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

Chain B from PDB  Type:PROTEIN  Length:313
 aligned with IUNH_CRIFA | Q27546 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:313
                                    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   
           IUNH_CRIFA     2 PKKIILDCDPGLDDAVAILLAHGNPEIELLAITTVVGNQTLAKVTRNAQLVADIAGITGVPIAAGCDKPLVRKIMTAGHIHGESGMGTVAYPAEFKNKVDERHAVNLIIDLVMSHEPKTITLVPTGGLTNIAMAARLEPRIVDRVKEVVLMGGGYHEGNATSVAEFNIIIDPEAAHIVFNESWQVTMVGLDLTHQALATPPILQRVKEVDTNPARFMLEIMDYYTKIYQSNRYMAAAAVHDPCAVAYVIDPSVMTTERVPVDIELTGKLTLGMTVADFRNPRPEHCHTQVAVKLDFEKFWGLVLDALERIGDP 314
               SCOP domains d2masb_ B: Inosine-uridine nucleoside N-ribohydrolase, IU-NH                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2masB00 B:2-314 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhh......eeee.............hhhh......................hhhhhhhhhhh.....eeeee....hhhhhhhhh.hhhhhheeeeeee..............hhhhhhhhhhhhhhh....eeee.hhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.hhh......eeee..........eeee..........eee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------IUNH       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mas B   2 AKKIILDCDPGLDDAVAILLAHGNPEIELLAITTVVGNQTLAKVTRNAQLVADIAGITGVPIAAGCDKPLVRKIMTAGHIHGESGMGTVAYPAEFKNKVDERHAVNLIIDLVMSHEPKTITLVPTGGLTNIAMAARLEPRIVDRVKEVVLMGGGYHEGNATSVAEFNIIIDPEAAHIVFNESWQVTMVGLDLTHQALATPPILQRVKEVDTNPARFMLEIMDYYTKIYQSNRYMAAAAVHDPCAVAYVIDPSVMTTERVPVDIELTGKLTLGMTVADFRNPRPEHCHTQVAVKLDFEKFWGLVLDALERIGDP 314
                                    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

Chain C from PDB  Type:PROTEIN  Length:313
 aligned with IUNH_CRIFA | Q27546 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:313
                                    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   
           IUNH_CRIFA     2 PKKIILDCDPGLDDAVAILLAHGNPEIELLAITTVVGNQTLAKVTRNAQLVADIAGITGVPIAAGCDKPLVRKIMTAGHIHGESGMGTVAYPAEFKNKVDERHAVNLIIDLVMSHEPKTITLVPTGGLTNIAMAARLEPRIVDRVKEVVLMGGGYHEGNATSVAEFNIIIDPEAAHIVFNESWQVTMVGLDLTHQALATPPILQRVKEVDTNPARFMLEIMDYYTKIYQSNRYMAAAAVHDPCAVAYVIDPSVMTTERVPVDIELTGKLTLGMTVADFRNPRPEHCHTQVAVKLDFEKFWGLVLDALERIGDP 314
               SCOP domains d2masc_ C: Inosine-uridine nucleoside N-ribohydrolase, IU-NH                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2masC00 C:2-314 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhh......eeee.............hhhh......................hhhhhhhhhhh.....eeeee....hhhhhhhhh.hhhhhh...eeee..............hhhhhhhhhhhhhhh....eeee.hhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhh..eee.eeee..........eeee..........eeee....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------IUNH       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mas C   2 AKKIILDCDPGLDDAVAILLAHGNPEIELLAITTVVGNQTLAKVTRNAQLVADIAGITGVPIAAGCDKPLVRKIMTAGHIHGESGMGTVAYPAEFKNKVDERHAVNLIIDLVMSHEPKTITLVPTGGLTNIAMAARLEPRIVDRVKEVVLMGGGYHEGNATSVAEFNIIIDPEAAHIVFNESWQVTMVGLDLTHQALATPPILQRVKEVDTNPARFMLEIMDYYTKIYQSNRYMAAAAVHDPCAVAYVIDPSVMTTERVPVDIELTGKLTLGMTVADFRNPRPEHCHTQVAVKLDFEKFWGLVLDALERIGDP 314
                                    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

Chain D from PDB  Type:PROTEIN  Length:313
 aligned with IUNH_CRIFA | Q27546 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:313
                                    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   
           IUNH_CRIFA     2 PKKIILDCDPGLDDAVAILLAHGNPEIELLAITTVVGNQTLAKVTRNAQLVADIAGITGVPIAAGCDKPLVRKIMTAGHIHGESGMGTVAYPAEFKNKVDERHAVNLIIDLVMSHEPKTITLVPTGGLTNIAMAARLEPRIVDRVKEVVLMGGGYHEGNATSVAEFNIIIDPEAAHIVFNESWQVTMVGLDLTHQALATPPILQRVKEVDTNPARFMLEIMDYYTKIYQSNRYMAAAAVHDPCAVAYVIDPSVMTTERVPVDIELTGKLTLGMTVADFRNPRPEHCHTQVAVKLDFEKFWGLVLDALERIGDP 314
               SCOP domains d2masd_ D: Inosine-uridine nucleoside N-ribohydrolase, IU-NH                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2masD00 D:2-314 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) -IU_nuc_hydro-2masD01 D:3-312                                                                                                                                                                                                                                                                                          -- Pfam domains (1)
           Pfam domains (2) -IU_nuc_hydro-2masD02 D:3-312                                                                                                                                                                                                                                                                                          -- Pfam domains (2)
           Pfam domains (3) -IU_nuc_hydro-2masD03 D:3-312                                                                                                                                                                                                                                                                                          -- Pfam domains (3)
           Pfam domains (4) -IU_nuc_hydro-2masD04 D:3-312                                                                                                                                                                                                                                                                                          -- Pfam domains (4)
         Sec.struct. author .eeeeeee...hhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhh......eeee.............hhhh......................hhhhhhhhhhh.....eeeee....hhhhhhhhh.hhhhhh...eeee..............hhhhhhhhhhhhhhh....eeee.hhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.hhh..eee.eeee..........eeee..........eeee....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------IUNH       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mas D   2 AKKIILDCDPGLDDAVAILLAHGNPEIELLAITTVVGNQTLAKVTRNAQLVADIAGITGVPIAAGCDKPLVRKIMTAGHIHGESGMGTVAYPAEFKNKVDERHAVNLIIDLVMSHEPKTITLVPTGGLTNIAMAARLEPRIVDRVKEVVLMGGGYHEGNATSVAEFNIIIDPEAAHIVFNESWQVTMVGLDLTHQALATPPILQRVKEVDTNPARFMLEIMDYYTKIYQSNRYMAAAAVHDPCAVAYVIDPSVMTTERVPVDIELTGKLTLGMTVADFRNPRPEHCHTQVAVKLDFEKFWGLVLDALERIGDP 314
                                    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

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: Nucleoside hydrolase (27)

Superfamily: Nucleoside hydrolase (27)

Family: Nucleoside hydrolase (22)

Protein domain: Inosine-uridine nucleoside N-ribohydrolase, IU-NH (2)

Crithidia fasciculata [TaxId: 5656] (2)

1a	d2masa_	A:
1b	d2masb_	B:
1c	d2masc_	C:
1d	d2masd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Inosine-uridine Nucleoside N-ribohydrolase; Chain A (17)

Homologous Superfamily: Inosine-uridine Nucleoside N-ribohydrolase, chain A (17)

Crithidia fasciculata. Organism_taxid: 5656. (2)

1a	2masA00	A:2-314
1b	2masB00	B:2-314
1c	2masC00	C:2-314
1d	2masD00	D:2-314

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: IU_nuc_hydro] (7)

Family: IU_nuc_hydro (7)

Crithidia fasciculata (2)

1a	IU_nuc_hydro-2masD01	D:3-312
1b	IU_nuc_hydro-2masD02	D:3-312
1c	IU_nuc_hydro-2masD03	D:3-312
1d	IU_nuc_hydro-2masD04	D:3-312

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (IUNH_CRIFA | Q27546)

molecular function
	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:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds	Catalysis of the hydrolysis of any N-glycosyl bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).

Asymmetric/Biological Unit
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	2mas
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	IUNH_CRIFA \| Q27546	:	1mas

(no "Related Entries Specified in the PDB File" available for 2MAS)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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