1YNY - JenaLib

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Title :   MOLECULAR STRUCTURE OF D-HYDANTOINASE FROM A BACILLUS SP. AR9: EVIDENCE FOR MERCURY INHIBITION

Authors :   K. V. Radha Kishan, R. M. Vohra, K. Ganeshan, V. Agrawal, V. M. Sharma, R

Date :   26 Jan 05 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Tim-Barrel; Hydantoinase; Binuclear Metal-Binding; Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. V. Radha Kishan, R. M. Vohra, K. Ganesan, V. Agrawal, V. M. Sharma, R. Sharma
Molecular Structure Of D-Hydantoinase From Bacillus Sp. Ar9 Evidence For Mercury Inhibition.
J. Mol. Biol. V. 347 95 2005
PubMed-ID: 15733920 | Reference-DOI: 10.1016/J.JMB.2005.01.025
(for further references see the PDB file header)

Molecule 1 - D-HYDANTOINASE
	Chains	:	A, B
	EC Number	:	3.5.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS SP.
	Organism Taxid	:	301298
	Strain	:	AR9
	Synonym	:	DIHYDROPYRIMIDINASE; DHPASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:58 , HIS A:60 , LYS A:150 , ASP A:315 , MN A:472 , HOH A:1128	BINDING SITE FOR RESIDUE MN A 471
2	AC2	SOFTWARE	LYS A:150 , HIS A:183 , HIS A:239 , MN A:471 , HOH A:1112 , HOH A:1128	BINDING SITE FOR RESIDUE MN A 472
3	AC3	SOFTWARE	HIS B:58 , HIS B:60 , LYS B:150 , ASP B:315 , MN B:472 , HOH B:5110	BINDING SITE FOR RESIDUE MN B 471
4	AC4	SOFTWARE	LYS B:150 , HIS B:183 , HIS B:239 , MN B:471 , HOH B:5109 , HOH B:5110	BINDING SITE FOR RESIDUE MN B 472

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

Asymmetric Unit

No.	Residues
1	Ser A:288	-	Pro A:289
2	Phe A:379	-	Pro A:380
3	Ser B:288	-	Pro B:289
4	Phe B:379	-	Pro B:380

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

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

(no "Exon" information available for 1YNY)

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:455
 aligned with Q5DLU2_9BACI | Q5DLU2 from UniProtKB/TrEMBL  Length:461

    Alignment length:459
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451         
         Q5DLU2_9BACI     2 KKWIRGGTVVTAADTYQADVLIEGERVVAIGHQLSVNGAEEIDATGCYVIPGGIDPHTHLDMPFGGTVTADDFFTGTRAAAFGGTTSIVDFCLTKKGESLKSAIATWHEKARGKAVIDYGFHLMIAEANDQVLEELESVISSEGITSLKVFMAYKNVFQADDETLFKTLVKAKELGALVQVHAENGDVLDYLTKKALAEGNTDPIYHAYTRPPEAEGEATGRAIALTALAGSQLYVVHVSCASAVQRIAEAREKGWNVYGETCPQYLALDVSIMDQPDFEGAKYVWSPPLREKWNQEVLWSALKNGILQTVGSDHCPFNFRGQKELGRGDFTKIPNGGPLIEDRLTILYSEGVRQGRISLNQFVDISSTKAAKLFGMFPRKGTIAVGSDADIVIFDPHVKRTLSVETHHMNVDYNPFEGMEVYGEVVSVLSRGSFVVRDKQFVGQAGSGQYIKRTTFEQ 460
               SCOP domains d1ynya1 A:2-52,A:385-460 D-hydant    oinase        d1ynya2 A:53-384 D-hydantoinase                                                                                                                                                                                                                                                                                                             d1ynya1 A:2-52,A:385-460 D-hydantoinase                                      SCOP domains
               CATH domains 1ynyA01 A:2-52,A:381-460                           1ynyA02 A:53-380 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                             1ynyA01 A:2-52,A:381-460 Urease, subunit C, domain 1                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee....eee.eeeee..eeeeee..----..eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhh....ee...........hhhhhh.hhhhh........hhhhhhhhhh......hhhhhhhhhhhhhhhhh................eeeeeeeeeeee................eeeeeeeeeeee..eeeee..ee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yny A   2 KKWIRGGTVVTAADTYQADVLIEGERVVAIGHQ----GAEEIDATGCYVIPGGIDPHTHLDMPFGGTVTADDFFTGTRAAAFGGTTSIVDFCLTKKGESLKSAIATWHEKARGKAVIDYGFHLMIAEANDQVLEELESVISSEGITSLKVFMAYKNVFQADDETLFKTLVKAKELGALVQVHAENGDVLDYLTKKALAEGNTDPIYHAYTRPPEAEGEATGRAIALTALAGSQLYVVHVSCASAVQRIAEAREKGWNVYGETCPQYLALDVSIMDQPDFEGAKYVWSPPLREKWNQEVLWSALKNGILQTVGSDHCPFNFRGQKELGRGDFTKIPNGGPLIEDRLTILYSEGVRQGRISLNQFVDISSTKAAKLFGMFPRKGTIAVGSDADIVIFDPHVKRTLSVETHHMNVDYNPFEGMEVYGEVVSVLSRGSFVVRDKQFVGQAGSGQYIKRTTFEQ 460
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451         
                                                           34   39

Chain B from PDB  Type:PROTEIN  Length:459
 aligned with Q5DLU2_9BACI | Q5DLU2 from UniProtKB/TrEMBL  Length:461

    Alignment length:459
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451         
         Q5DLU2_9BACI     2 KKWIRGGTVVTAADTYQADVLIEGERVVAIGHQLSVNGAEEIDATGCYVIPGGIDPHTHLDMPFGGTVTADDFFTGTRAAAFGGTTSIVDFCLTKKGESLKSAIATWHEKARGKAVIDYGFHLMIAEANDQVLEELESVISSEGITSLKVFMAYKNVFQADDETLFKTLVKAKELGALVQVHAENGDVLDYLTKKALAEGNTDPIYHAYTRPPEAEGEATGRAIALTALAGSQLYVVHVSCASAVQRIAEAREKGWNVYGETCPQYLALDVSIMDQPDFEGAKYVWSPPLREKWNQEVLWSALKNGILQTVGSDHCPFNFRGQKELGRGDFTKIPNGGPLIEDRLTILYSEGVRQGRISLNQFVDISSTKAAKLFGMFPRKGTIAVGSDADIVIFDPHVKRTLSVETHHMNVDYNPFEGMEVYGEVVSVLSRGSFVVRDKQFVGQAGSGQYIKRTTFEQ 460
               SCOP domains d1ynyb1 B:2-52,B:385-460 D-hydantoinase            d1ynyb2 B:53-384 D-hydantoinase                                                                                                                                                                                                                                                                                                             d1ynyb1 B:2-52,B:385-460 D-hydantoinase                                      SCOP domains
               CATH domains 1ynyB01 B:2-52,B:381-460                           1ynyB02 B:53-380 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                             1ynyB01 B:2-52,B:381-460 Urease, subunit C, domain 1                             CATH domains
           Pfam domains (1) ------------------------------------------Amidohydro_4-1ynyB01 B:44-394                                                                                                                                                                                                                                                                                                                                  ------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------Amidohydro_4-1ynyB02 B:44-394                                                                                                                                                                                                                                                                                                                                  ------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeee..eee....eee.eeee....eeeee........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee........hhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhh....ee...........hhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yny B   2 KKWIRGGTVVTAADTYQADVLIEGERVVAIGHQLSVNGAEEIDATGCYVIPGGIDPHTHLDMPFGGTVTADDFFTGTRAAAFGGTTSIVDFCLTKKGESLKSAIATWHEKARGKAVIDYGFHLMIAEANDQVLEELESVISSEGITSLKVFMAYKNVFQADDETLFKTLVKAKELGALVQVHAENGDVLDYLTKKALAEGNTDPIYHAYTRPPEAEGEATGRAIALTALAGSQLYVVHVSCASAVQRIAEAREKGWNVYGETCPQYLALDVSIMDQPDFEGAKYVWSPPLREKWNQEVLWSALKNGILQTVGSDHCPFNFRGQKELGRGDFTKIPNGGPLIEDRLTILYSEGVRQGRISLNQFVDISSTKAAKLFGMFPRKGTIAVGSDADIVIFDPHVKRTLSVETHHMNVDYNPFEGMEVYGEVVSVLSRGSFVVRDKQFVGQAGSGQYIKRTTFEQ 460
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Metal-dependent hydrolases (190)

Ar9 (Bacillus sp) (1)

1a	1ynyA02	A:53-380
1b	1ynyB02	B:53-380

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Urease, subunit C; domain 1 (95)

Homologous Superfamily: Urease, subunit C, domain 1 (95)

Ar9 (Bacillus sp) (1)

2a	1ynyA01	A:2-52,A:381-460
2b	1ynyB01	B:2-52,B:381-460

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_4 (8)

Bacillus sp. AR9 (1)

1a	Amidohydro_4-1ynyB01	B:44-394
1b	Amidohydro_4-1ynyB02	B:44-394

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q5DLU2_9BACI | Q5DLU2)

molecular function
	GO:0004157	dihydropyrimidinase activity	Catalysis of the reaction: 5,6-dihydrouracil + H2O = 3-ureidopropionate.
	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:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:379 - Pro A:380	[ RasMol ]
		Phe B:379 - Pro B:380	[ RasMol ]
		Ser A:288 - Pro A:289	[ RasMol ]
		Ser B:288 - Pro B:289	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1YNY)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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