3UBP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE

Authors :   S. Benini, W. R. Rypniewski, K. S. Wilson, S. Miletti, S. Mangani, S. Ciu

Date :   16 Dec 98 (Deposition) - 17 Dec 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: A,B,C  (3x)

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

Reference :   S. Benini, W. R. Rypniewski, K. S. Wilson, S. Miletti, S. Ciurli, S. Mangani
A New Proposal For Urease Mechanism Based On The Crystal Structures Of The Native And Inhibited Enzyme From Bacillus Pasteurii: Why Urea Hydrolysis Costs Two Nickels.
Structure Fold. Des. V. 7 205 1999
PubMed-ID: 10368287 | Reference-DOI: 10.1016/S0969-2126(99)80026-4
(for further references see the PDB file header)

Molecule 1 - PROTEIN (UREASE GAMMA SUBUNIT)
	Cellular Location	:	CYTOPLASM
	Chains	:	A
	EC Number	:	3.5.1.5
	Organism Scientific	:	SPOROSARCINA PASTEURII
	Organism Taxid	:	1474
	Strain	:	DSM 33
	Synonym	:	UREA AMINOHYDROLASE

Molecule 2 - PROTEIN (UREASE BETA SUBUNIT)
	Cellular Location	:	CYTOPLASM
	Chains	:	B
	EC Number	:	3.5.1.5
	Organism Scientific	:	SPOROSARCINA PASTEURII
	Organism Taxid	:	1474
	Strain	:	DSM 33
	Synonym	:	UREA AMINOHYDROLASE

Molecule 3 - PROTEIN (UREASE ALPHA SUBUNIT)
	Cellular Location	:	CYTOPLASM
	Chains	:	C
	EC Number	:	3.5.1.5
	Organism Scientific	:	SPOROSARCINA PASTEURII
	Organism Taxid	:	1474
	Strain	:	DSM 33
	Synonym	:	UREA AMINOHYDROLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	2PA	1	Ligand/Ion	DIAMIDOPHOSPHATE
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	NI	2	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	2PA	1	Ligand/Ion	DIAMIDOPHOSPHATE
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (3, 9)

No.	Name	Count	Type	Full Name
1	2PA	3	Ligand/Ion	DIAMIDOPHOSPHATE
2	ACE	3	Mod. Amino Acid	ACETYL GROUP
3	KCX	3	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , 2PA C:902	BINDING SITE FOR RESIDUE NI C 900
2	AC2	SOFTWARE	HIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , 2PA C:902	BINDING SITE FOR RESIDUE NI C 901
3	AC3	SOFTWARE	HIS C:137 , HIS C:139 , ALA C:170 , KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , HIS C:323 , ASP C:363 , ALA C:366 , MET C:367 , NI C:900 , NI C:901	BINDING SITE FOR RESIDUE 2PA C 902
4	CAT	AUTHOR	HIS C:137 , HIS C:139 , KCX C:220 , HIS C:249 , HIS C:275 , ASP C:363	THE DINUCLEAR NICKEL 2+ METALLOCENTER IS INHIBITED BY A MOLECULE OF DIAMIDOPHOSPHATE, MIMICKING THE TETRAHEDRAL TRANSITION STATE OF UREA HYDROLYSIS

(no "SS Bond" information available for 3UBP)

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 3UBP)

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, 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 2 (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 3UBP)

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:101
 aligned with URE3_SPOPA | P41022 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:101
                             1                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99 
           URE3_SPOPA     - -MHLNPAEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS 100
               SCOP domains d3ubpa_ A: Urease, gamma-subunit                                                                      SCOP domains
               CATH domains -3ubpA00 A:1-100 Urease, subunit A                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhh..hhhhhh.eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3ubp A   0 xMHLNPAEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS 100
                            |        9        19        29        39        49        59        69        79        89        99 
                            0-ACE

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 d3ubpb_ B: Urease, beta-subunit                                                                                            SCOP domains
               CATH domains 3ubpB00 B:5-126 Urease, subunit B                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....eee......eeeeeeee.....eeee...hhhhh...ee.hhhhhh.eee......eeee....eeeeeeee.....ee........ee..hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ubp 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 d3ubpc1 C:1-131,C:435-483 alpha-Subunit of urease                                                                                  d3ubpc2 C:132-434,C:484-570 alpha-subunit of urease, catalytic domain                                                                                                                                                                                                                                          d3ubpc1 C:1-131,C:435-483 alpha-Subunit of ureased3ubpc2 C:132-434,C:484-570 alpha-subunit of urease, catalytic domain                   SCOP domains
               CATH domains 3ubpC01 C:1-131,C:426-483 Urease, subunit C, domain 1                                                                              3ubpC02 C:132-425,C:484-569 Metal-dependent hydrolases                                                                                                                                                                                                                                                3ubpC01 C:1-131,C:426-483 Urease, subunit C, domain 1     3ubpC02 C:132-425,C:484-569 Metal-dependent hydrolases                                - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhh.....eee......eee......................................eeeeeeeeee..eeeeeeeeee..eeeeee.....................eeee....eeee.eeeeeee....hhhhhhhhh.eeeeeee....hhhhhhh...hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhh...eeeee.hhh.hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhh...eee............hhhhhhhh..eee...........hhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh...............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
                 3ubp 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)
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		→ 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 "Pfam Domain" information available for 3UBP)

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 Units
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	3ubp
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(no "Related Entries Specified in the PDB File" available for 3UBP)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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