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Title :   STRUCTURE OF ALLANTOICASE

Authors :   N. Leulliot, S. Quevillon-Cheruel, I. Sorel, M. Graille, P. Meyer, D. Liger, K. Blondeau, J. Janin, H. Van Tilbeurgh

Date :   23 Feb 04 (Deposition) - 02 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Allantoicase, Jelly Roll, Hexamer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Leulliot, S. Quevillon-Cheruel, I. Sorel, M. Graille, P. Meyer, D. Liger, K. Blondeau, J. Janin, H. Van Tilbeurgh
Crystal Structure Of Yeast Allantoicase Reveals A Repeated Jelly Roll Motif
J. Biol. Chem. V. 279 23447 2004
PubMed-ID: 15020593 | Reference-DOI: 10.1074/JBC.M401336200
(for further references see the PDB file header)

Molecule 1 - ALLANTOICASE
	Chains	:	A, B
	EC Number	:	3.5.3.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DAL2, ALC1, YIR029W
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	ALLANTOATE AMIDINOHYDROLASE

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1SG3)

(no "Site" information available for 1SG3)

(no "SS Bond" information available for 1SG3)

Asymmetric Unit

No.	Residues
1	Tyr A:170	-	Pro A:171
2	Ile A:330	-	Pro A:331
3	Tyr B:170	-	Pro B:171
4	Ile B:330	-	Pro B:331

(no "SAP(SNP)/Variant" information available for 1SG3)

(no "PROSITE Motif" information available for 1SG3)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YIR029W	1	YIR029W.1	IX:410804-411835	1032	ALLC_YEAST	1-343	343	2	A:1-343 (gaps) B:1-343 (gaps)	343 343

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:317
 aligned with ALLC_YEAST | P25335 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:343
                                    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       320       330       340   
           ALLC_YEAST     1 MKFFSLADEAEFKSIIISKNKAVDVIGSKLGGQVVSFSDEWFASAENLIQPTAPIRDPTRFVHSGAWYDGWETRRHNEMEYDWVIIKMGVAAAHIIGGEIDTAFFNGNHAPFVSIEALYDEGEEGNIVEDDSRWVEIVEKFECGPSQRHLFVRGNGLTKERFTHIKLKMYPDGGIARFRLYGRVVPPELKTKDHIIDLAYVCNGAVALKYSDQHFGSVDNLLLPGRGHDMSDGWETKRSRQPGHTDWAVIQLGRESSFIEKIIVDTAHFRGNFPQFITVEGCLKESESSENTGEGTWVELVGKSKTGPDKEHVYEIRKSIRVSHVKLTIIPDGGVKRIRVWGY 343
               SCOP domains d1sg3a1 A:1-187 Allantoicase                                                                                                                                                                      d1sg3a2 A:195-343 Allantoicase                                                                                                                        SCOP domains
               CATH domains -1sg3A01 A:2-187 Galactose-binding domain-like                                                                                                                                                    1sg3A02 A:195-343 Galactose-binding domain-like                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhh.....ee..hhhhh.eeeee......hhhhhhh.......---------....ee.........eeeeee.....eeeeeeeee..........eeeeeee................eeeeeeee.....eeeee...........eeeeeee...ee.eeeeeeee...-------.ee..hhhhh.eeeee......hhhhh.......hhhhhee..........eeeeee......eeeeeeee..........eeeeeee..----------...eeeeeeee.....eeeeeeeee....eeeeeee...ee.eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-343 (gaps) UniProt: 1-343                                                                                                                                                                                                                                                                                                            Transcript 1
                 1sg3 A   1 MKFFSLADEAEFKSIIISKNKAVDVIGSKLGGQVVSFSDEWFASAENLIQPTAPIRD---------WYDGWETRRHNEMEYDWVIIKMGVAAAHIIGGEIDTAFFNGNHAPFVSIEALYDEGEEGNIVEDDSRWVEIVEKFECGPSQRHLFVRGNGLTKERFTHIKLKMYPDGGIARFRLYGRVVPP-------IIDLAYVCNGAVALKYSDQHFGSVDNLLLPGRGHDMSDGWETKRSRQPGHTDWAVIQLGRESSFIEKIIVDTAHFRGNFPQFITVEGCLK----------GTWVELVGKSKTGPDKEHVYEIRKSIRVSHVKLTIIPDGGVKRIRVWGY 343
                                    10        20        30        40        50      |  -      | 70        80        90       100       110       120       130       140       150       160       170       180      |  -    |  200       210       220       230       240       250       260       270       280   |     -    |  300       310       320       330       340   
                                                                                   57        67                                                                                                                     187     195                                                                                      284        295

Chain B from PDB  Type:PROTEIN  Length:317
 aligned with ALLC_YEAST | P25335 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:344
                                                                                                                                                                                                                                                                                                                                                                                343 
                                    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       320       330       340  | 
           ALLC_YEAST     1 MKFFSLADEAEFKSIIISKNKAVDVIGSKLGGQVVSFSDEWFASAENLIQPTAPIRDPTRFVHSGAWYDGWETRRHNEMEYDWVIIKMGVAAAHIIGGEIDTAFFNGNHAPFVSIEALYDEGEEGNIVEDDSRWVEIVEKFECGPSQRHLFVRGNGLTKERFTHIKLKMYPDGGIARFRLYGRVVPPELKTKDHIIDLAYVCNGAVALKYSDQHFGSVDNLLLPGRGHDMSDGWETKRSRQPGHTDWAVIQLGRESSFIEKIIVDTAHFRGNFPQFITVEGCLKESESSENTGEGTWVELVGKSKTGPDKEHVYEIRKSIRVSHVKLTIIPDGGVKRIRVWGY-   -
               SCOP domains d1sg3b1 B:1-187 Allantoicase                                                                                                                                                                      d1sg3b2 B:195-344 Allantoicase                                                                                                                         SCOP domains
               CATH domains -1sg3B01 B:2-187 Galactose-binding domain-like                                                                                                                                                    1sg3B02 B:195-344 Galactose-binding domain-like                                                                                                        CATH domains
           Pfam domains (1) ---------------------------------------------------------         -------------------------------------------------------------------------------------------------------------------------       ---------Allantoicase-1sg3B01 B:204-342                                                                                                             -- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------         -------------------------------------------------------------------------------------------------------------------------       ---------Allantoicase-1sg3B02 B:204-342                                                                                                             -- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------         -------------------------------------------------------------------------------------------------------------------------       ---------Allantoicase-1sg3B03 B:204-342                                                                                                             -- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------         -------------------------------------------------------------------------------------------------------------------------       ---------Allantoicase-1sg3B04 B:204-342                                                                                                             -- Pfam domains (4)
         Sec.struct. author .eeehhhhhhhhhhhhh.....ee..hhhhh.eeeee......hhhhhhh.......---------....ee.........eeeeee.....eeeeeeeee..........eeeeeee................eeeeeeee.....eeeee...........eeeeeee...ee.eeeeeeee...-------.ee..hhhhh.eeeee......hhhhh.......hhhhhee..........eeeeee.......eeeeeee..........eeeeeee..-----------..eeeeeeee.....eeeeeeee.....eeeeeee...ee.eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-343 (gaps) UniProt: 1-343                                                                                                                                                                                                                                                                                                           - Transcript 1
                 1sg3 B   1 MKFFSLADEAEFKSIIISKNKAVDVIGSKLGGQVVSFSDEWFASAENLIQPTAPIRD---------WYDGWETRRHNEMEYDWVIIKMGVAAAHIIGGEIDTAFFNGNHAPFVSIEALYDEGEEGNIVEDDSRWVEIVEKFECGPSQRHLFVRGNGLTKERFTHIKLKMYPDGGIARFRLYGRVVPP-------IIDLAYVCNGAVALKYSDQHFGSVDNLLLPGRGHDMSDGWETKRSRQPGHTDWAVIQLGRESSFIEKIIVDTAHFRGNFPQFITVEGCLK-----------TWVELVGKSKTGPDKEHVYEIRKSIRVSHVKLTIIPDGGVKRIRVWGYH 344
                                    10        20        30        40        50      |  -      | 70        80        90       100       110       120       130       140       150       160       170       180      |  -    |  200       210       220       230       240       250       260       270       280   |     -     | 300       310       320       330       340    
                                                                                   57        67                                                                                                                     187     195                                                                                      284         296

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: All beta proteins (24004)

Fold: Galactose-binding domain-like (314)

Superfamily: Galactose-binding domain-like (314)

Family: Allantoicase repeat (2)

Protein domain: Allantoicase (2)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d1sg3a1	A:1-187
1b	d1sg3a2	A:195-343
1c	d1sg3b1	B:1-187
1d	d1sg3b2	B:195-344

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Galactose-binding domain-like (195)

Baker's yeast (Saccharomyces cerevisiae) (6)

1a	1sg3A01	A:2-187
1b	1sg3A02	A:195-343
1c	1sg3B02	B:195-344
1d	1sg3B01	B:2-187

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GBD (153)

Family: Allantoicase (2)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (2)

1a	Allantoicase-1sg3B01	B:204-342
1b	Allantoicase-1sg3B02	B:204-342
1c	Allantoicase-1sg3B03	B:204-342
1d	Allantoicase-1sg3B04	B:204-342

Asymmetric Unit(hide GO term definitions)

Chain A,B (ALLC_YEAST | P25335)

molecular function
	GO:0004037	allantoicase activity	Catalysis of the reaction: allantoate + H(2)O = (S)-ureidoglycolate + urea.
	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.
biological process
	GO:0000256	allantoin catabolic process	The chemical reactions and pathways resulting in the breakdown of allantoin, (2,5-dioxo-4-imidazolidinyl)urea.
	GO:0006144	purine nucleobase metabolic process	The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ile A:330 - Pro A:331	[ RasMol ]
		Ile B:330 - Pro B:331	[ RasMol ]
		Tyr A:170 - Pro A:171	[ RasMol ]
		Tyr B:170 - Pro B:171	[ RasMol ]

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Ligands, Modified Residues, Ions (0, 0)

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