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Title :   THE CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE IN COMPLEX WITH CITRATE

Authors :   S. Benini, P. Kosikowska, M. Cianci, A. Gonzalez Vara, L. Berlicki, S.

Date :   14 Dec 11 (Deposition) - 16 Jan 13 (Release) - 03 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Hydrolase, Bacillus Pasteurii (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Benini, P. Kosikowska, M. Cianci, L. Mazzei, A. G. Vara, L. Berlicki S. Ciurli
The Crystal Structure Of Sporosarcina Pasteurii Urease In A Complex With Citrate Provides New Hints For Inhibitor Design.
J. Biol. Inorg. Chem. V. 18 391 2013
PubMed-ID: 23412551 | Reference-DOI: 10.1007/S00775-013-0983-7
(for further references see the PDB file header)

Molecule 1 - UREASE SUBUNIT GAMMA
	Chains	:	A
	EC Number	:	3.5.1.5
	Organism Scientific	:	SPOROSARCINA PASTEURII
	Organism Taxid	:	1474
	Strain	:	DSM33
	Synonym	:	UREA AMIDOHYDROLASE SUBUNIT GAMMA

Molecule 2 - UREASE SUBUNIT BETA
	Chains	:	B
	EC Number	:	3.5.1.5
	Organism Scientific	:	SPOROSARCINA PASTEURII
	Organism Taxid	:	1474
	Strain	:	DSM33
	Synonym	:	UREA AMIDOHYDROLASE SUBUNIT BETA

Molecule 3 - UREASE SUBUNIT ALPHA
	Chains	:	C
	EC Number	:	3.5.1.5
	Organism Scientific	:	SPOROSARCINA PASTEURII
	Organism Taxid	:	1474
	Strain	:	DSM33
	Synonym	:	UREA AMIDOHYDROLASE SUBUNIT ALPHA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 20)

No.	Name	Count	Type	Full Name
1	CXM	1	Mod. Amino Acid	N-CARBOXYMETHIONINE
2	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	FLC	1	Ligand/Ion	CITRATE ANION
4	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
5	NI	2	Ligand/Ion	NICKEL (II) ION
6	OH	1	Ligand/Ion	HYDROXIDE ION
7	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (5, 51)

No.	Name	Count	Type	Full Name
1	CXM	3	Mod. Amino Acid	N-CARBOXYMETHIONINE
2	EDO	30	Ligand/Ion	1,2-ETHANEDIOL
3	FLC	3	Ligand/Ion	CITRATE ANION
4	KCX	3	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
5	NI	-1	Ligand/Ion	NICKEL (II) ION
6	OH	-1	Ligand/Ion	HYDROXIDE ION
7	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:50 , LYS A:51 , THR A:52 , PHE A:86 , ASP A:88 , HOH A:2092 , HOH A:2093 , VAL C:309 , ASN C:310 , LYS C:559	BINDING SITE FOR RESIDUE EDO A1101
02	AC2	SOFTWARE	LYS A:29 , ASP A:67 , ASP A:68 , HOH A:2033 , HOH A:2038	BINDING SITE FOR RESIDUE EDO A1102
03	AC3	SOFTWARE	ASN A:4 , ALA A:6 , LYS A:10 , HOH A:2005 , HOH A:2084 , PHE C:568 , PHE C:570 , HOH C:2294	BINDING SITE FOR RESIDUE EDO A1103
04	AC4	SOFTWARE	ASP B:101 , HOH B:2141 , PRO C:229 , HOH C:2214	BINDING SITE FOR RESIDUE EDO B1127
05	AC5	SOFTWARE	ARG B:116	BINDING SITE FOR RESIDUE SO4 B1128
06	AC6	SOFTWARE	KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , NI C:601 , OH C:1571 , FLC C:1572	BINDING SITE FOR RESIDUE NI C 600
07	AC7	SOFTWARE	HIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , NI C:600 , OH C:1571 , FLC C:1572	BINDING SITE FOR RESIDUE NI C 601
08	AC8	SOFTWARE	HIS C:137 , KCX C:220 , HIS C:275 , ASP C:363 , NI C:600 , NI C:601 , FLC C:1572	BINDING SITE FOR RESIDUE OH C1571
09	AC9	SOFTWARE	HIS C:139 , LYS C:169 , ALA C:170 , KCX C:220 , HIS C:222 , ASP C:224 , HIS C:249 , GLY C:280 , ARG C:339 , ASP C:363 , ALA C:366 , MET C:367 , NI C:600 , NI C:601 , OH C:1571 , HOH C:2170 , HOH C:2209 , HOH C:2274	BINDING SITE FOR RESIDUE FLC C1572
10	BC1	SOFTWARE	ASP C:34 , THR C:36 , TYR C:38 , HOH C:2035 , HOH C:2050 , HOH C:2433	BINDING SITE FOR RESIDUE EDO C1573
11	BC2	SOFTWARE	ASP C:286 , ALA C:289 , ILE C:537 , ILE C:539 , HOH C:2234	BINDING SITE FOR RESIDUE EDO C1574
12	BC3	SOFTWARE	GLN B:41 , HOH B:2068 , GLY C:46 , LEU C:325 , HOH C:2276 , HOH C:2434	BINDING SITE FOR RESIDUE EDO C1575
13	BC4	SOFTWARE	TYR C:93 , GLU C:423 , GLN C:501 , ARG C:513 , ILE C:514 , HOH C:2435	BINDING SITE FOR RESIDUE EDO C1576
14	BC5	SOFTWARE	TYR C:35 , TYR C:83 , ILE C:97 , GLU C:429 , HOH C:2032 , HOH C:2436	BINDING SITE FOR RESIDUE EDO C1577
15	BC6	SOFTWARE	ARG C:62 , PRO C:177 , GLU C:181	BINDING SITE FOR RESIDUE EDO C1578
16	BC7	SOFTWARE	SER C:204 , ILE C:205 , HOH C:2084 , HOH C:2189 , HOH C:2194	BINDING SITE FOR RESIDUE SO4 C1579
17	BC8	SOFTWARE	VAL C:558 , LYS C:559 , GLU C:560 , HOH C:2422	BINDING SITE FOR RESIDUE SO4 C1580
18	BC9	SOFTWARE	LYS C:511	BINDING SITE FOR RESIDUE SO4 C1581

(no "SS Bond" information available for 4AC7)

Asymmetric Unit

No.	Residues
1	Ala C:284	-	Pro C:285
2	Arg C:305	-	Pro C:306
3	Gln C:472	-	Pro C:473

(no "SAP(SNP)/Variant" information available for 4AC7)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UREASE_1	PS01120	Urease nickel ligands signature.	URE1_SPOPA	129-142	1	C:130-143
2	UREASE_3	PS51368	Urease domain profile.	URE1_SPOPA	131-569	1	C:132-570
3	UREASE_2	PS00145	Urease active site.	URE1_SPOPA	319-335	1	C:320-336

Biological Unit 1 (3, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UREASE_1	PS01120	Urease nickel ligands signature.	URE1_SPOPA	129-142	3	C:130-143
2	UREASE_3	PS51368	Urease domain profile.	URE1_SPOPA	131-569	3	C:132-570
3	UREASE_2	PS00145	Urease active site.	URE1_SPOPA	319-335	3	C:320-336

(no "Exon" information available for 4AC7)

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:100
 aligned with URE3_SPOPA | P41022 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           URE3_SPOPA     1 MHLNPAEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS 100
               SCOP domains d4ac7a_ A: Urease, gamma-subunit                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhh...hhhhhh.eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4ac7 A   1 mHLNPAEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS 100
                            |       10        20        30        40        50        60        70        80        90       100
                            1-CXM

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with URE2_SPOPA | P41021 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:122
                                    14        24        34        44        54        64        74        84        94       104       114       124  
           URE2_SPOPA     5 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVEVNKELLFDRAEGIGRRLNIPSGTAARFEPGEEMEVELTELGGNREVFGISDLTNGSVDNKELILQRAKELGYKGVE 126
               SCOP domains d4ac7b_ B: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....eee......eeeeeeee.....eeee...hhhhh...ee.hhhhhh.eee......eeee....eeeeeeee.....ee........ee..hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ac7 B   5 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVEVNKELLFDRAEGIGRRLNIPSGTAARFEPGEEMEVELTELGGNREVFGISDLTNGSVDNKELILQRAKELGYKGVE 126
                                    14        24        34        44        54        64        74        84        94       104       114       124

Chain C from PDB  Type:PROTEIN  Length:570
 aligned with URE1_SPOPA | P41020 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:570
                                                        29                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                      28 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                    10        20       |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       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569
           URE1_SPOPA     1 MKINRQQYAESYGPTVGDRVRLADTDLG-EVEKDYYYLGDEVNFGGGKVLREGMGENGTYTRTENVLDLLLTNALILDYTGIYKADIGVKDGYIVGIGKGGNPDIMDGVTPNMIVGTATEVIAAEGKIVTAGGIDTHVHFINPDQVDVALANGITTLFGGGTGPAEGSKATTVTPGPWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGAAGLKIHEDWGATPASIDRSLTVADEADVQVAIHSDTLNEAGFLEDTVRAINGRVIHSFHVEGAGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIRPETIAAEDILHDLGIISMMSTDALAMGRAGEMVLRTWQTADKMKKQRGPLAEEKNGSDNFRLKRYVSKYTINPAIAQGMAHEVGSIEEGKFADLVLWEPKFFGVKADRVIKGGIIAYAQIGDPSASIPTPQPVMGRRMYGTVGDLIHDTNITFMSKSSIQQGVPAKLGLKRRIGTVKNCRNIGKKDMKWNDVTTDIDINPETYEVKVDGEVLTCEPVKELPMAQRYFLF 569
               SCOP domains d4ac7c1 C:1-131,C:435-483 alpha-Subunit of urease                                                                                  d4ac7c2 C:132-434,C:484-570 alpha-subunit of urease, catalytic domain                                                                                                                                                                                                                                          d4ac7c1 C:1-131,C:435-483 alpha-Subunit of ureased4ac7c2 C:132-434,C:484-570 alpha-subunit of urease, catalytic domain                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhh.....eee......eee......................................eeeeeeeeee..eeeeeeeeee..eeeeee.....................eeee....eeee.eeeeeee....hhhhhhhhh.eeeeeee....hhhhhhh...hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhh..eeeee.hhh.hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhh...eee............hhhhhhhh..eee..hhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh................eeeehhhhh.....eeee..eeeeeee.............eeee.hhhhhhhhhhh.eeeehhhhhhhhhhhhhh...eeee.......hhhhh........eee......eee..ee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------UREASE_1      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UREASE_2         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------UREASE_3  PDB: C:132-570 UniProt: 131-569                                                                                                                                                                                                                                                                                                                                                                                                               PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ac7 C   1 MKINRQQYAESYGPTVGDEVRLADTDLWIEVEKDYTTYGDEVNFGGGKVLREGMGENGTYTRTENVLDLLLTNALILDYTGIYKADIGVKDGYIVGIGKGGNPDIMDGVTPNMIVGTATEVIAAEGKIVTAGGIDTHVHFINPDQVDVALANGITTLFGGGTGPAEGSKATTVTPGPWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGAAGLkIHEDWGATPASIDRSLTVADEADVQVAIHSDTLNEAGFLEDTLRAINGRVIHSFHVEGAGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIRPETIAAEDILHDLGIISMMSTDALAMGRAGEMVLRTWQTADKMKKQRGPLAEEKNGSDNFRLKRYVSKYTINPAIAQGIAHEVGSIEEGKFADLVLWEPKFFGVKADRVIKGGIIAYAQIGDPSASIPTPQPVMGRRMYGTVGDLIHDTNITFMSKSSIQQGVPAKLGLKRRIGTVKNCRNIGKKDMKWNDVTTDIDINPETYEVKVDGEVLTCEPVKELPMAQRYFLF 570
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570
                                                                                                                                                                                                                                                     220-KCX

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 '\|'

(no "CATH Domain" information available for 4AC7)

(no "Pfam Domain" information available for 4AC7)

Asymmetric Unit(hide GO term definitions)

Chain A (URE3_SPOPA | P41022)

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:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	GO:0009039	urease activity	Catalysis of the reaction: urea + H2O = CO2 + 2 NH3.
biological process
	GO:0043419	urea catabolic process	The chemical reactions and pathways resulting in the breakdown of urea, the water soluble compound O=C-(NH2)2.
	GO:0019627	urea metabolic process	The chemical reactions and pathways involving urea, the water soluble compound O=C-(NH2)2.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B (URE2_SPOPA | P41021)

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:0009039	urease activity	Catalysis of the reaction: urea + H2O = CO2 + 2 NH3.
biological process
	GO:0043419	urea catabolic process	The chemical reactions and pathways resulting in the breakdown of urea, the water soluble compound O=C-(NH2)2.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain C (URE1_SPOPA | P41020)

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: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.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	GO:0009039	urease activity	Catalysis of the reaction: urea + H2O = CO2 + 2 NH3.
biological process
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
	GO:0043419	urea catabolic process	The chemical reactions and pathways resulting in the breakdown of urea, the water soluble compound O=C-(NH2)2.
	GO:0019627	urea metabolic process	The chemical reactions and pathways involving urea, the water soluble compound O=C-(NH2)2.
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
		Ala C:284 - Pro C:285	[ RasMol ]
		Arg C:305 - Pro C:306	[ RasMol ]
		Gln C:472 - Pro C:473	[ RasMol ]

Biological Unit
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	4ac7
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1ie7	PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTALSTRUCTURE
1s3t	BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE
1ubp	CRYSTAL STRUCTURE OF UREASE FROM BACILLUS PASTEURII INHIBITED WITH BETA-MERCAPTOETHANOL AT 1.65 ANGSTROMS RESOLUTION
2ubp	STRUCTURE OF NATIVE UREASE FROM BACILLUS PASTEURII
3ubp	DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE
4ubp	STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 20)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 19)

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Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File