1E9Y - JenaLib

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Title :   CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE IN COMPLEX WITH ACETOHYDROXAMIC ACID

Authors :   N. -C. Ha, S. -T. Oh, B. -H. Oh

Date :   01 Nov 00 (Deposition) - 01 Nov 01 (Release) - 25 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (12x)

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

Reference :   N. -C. Ha, S. -T. Oh, J. Y. Sung, K. -A. Cha, M. Hyung Lee, B. -H. Oh
Supramolecular Assembly And Acid Resistance Of Helicobacter Pylori Urease
Nat. Struct. Biol. V. 8 480 2001
PubMed-ID: 11373617 | Reference-DOI: 10.1038/88563

Molecule 1 - UREASE SUBUNIT ALPHA
	Chains	:	A
	EC Number	:	3.5.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210
	Synonym	:	UREA AMIDOHYDROLASE SUBUNIT ALPHA

Molecule 2 - UREASE SUBUNIT BETA
	Chains	:	B
	EC Number	:	3.5.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210
	Synonym	:	UREA AMIDOHYDROLASE SUBUNIT BETA

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (12x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	HAE	1	Ligand/Ion	ACETOHYDROXAMIC ACID
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	NI	2	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (2, 24)

No.	Name	Count	Type	Full Name
1	HAE	12	Ligand/Ion	ACETOHYDROXAMIC ACID
2	KCX	12	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:169 , KCX B:219 , HIS B:221 , HIS B:248 , HIS B:274 , GLY B:279 , ASP B:362 , ALA B:365 , NI B:3001 , NI B:3002	BINDING SITE FOR RESIDUE HAE B 800
2	AC2	SOFTWARE	KCX B:219 , HIS B:248 , HIS B:274 , GLY B:279 , HAE B:800 , NI B:3002	BINDING SITE FOR RESIDUE NI B3001
3	AC3	SOFTWARE	HIS B:136 , HIS B:138 , KCX B:219 , ASP B:362 , HAE B:800 , NI B:3001	BINDING SITE FOR RESIDUE NI B3002

(no "SS Bond" information available for 1E9Y)

Asymmetric Unit

No.	Residues
1	Ala B:283	-	Pro B:284
2	Ile B:304	-	Pro B:305
3	Gln B:471	-	Pro B:472

(no "SAP(SNP)/Variant" information available for 1E9Y)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UREASE_1	PS01120	Urease nickel ligands signature.	URE1_HELPY	129-142	1	B:129-142
2	UREASE_3	PS51368	Urease domain profile.	URE1_HELPY	131-569	1	B:131-569
3	UREASE_2	PS00145	Urease active site.	URE1_HELPY	319-335	1	B:319-335

Biological Unit 1 (3, 36)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UREASE_1	PS01120	Urease nickel ligands signature.	URE1_HELPY	129-142	12	B:129-142
2	UREASE_3	PS51368	Urease domain profile.	URE1_HELPY	131-569	12	B:131-569
3	UREASE_2	PS00145	Urease active site.	URE1_HELPY	319-335	12	B:319-335

(no "Exon" information available for 1E9Y)

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:238
 aligned with URE23_HELPY | P14916 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
          URE23_HELPY     1 MKLTPKELDKLMLHYAGELAKKRKEKGIKLNYVEAVALISAHIMEEARAGKKTAAELMQEGRTLLKPDDVMDGVASMIHEVGIEAMFPDGTKLVTVHTPIEANGKLVPGELFLKNEDITINEGKKAVSVKVKNVGDRPVQIGSHFHFFEVNRCLDFDREKTFGKRLDIASGTAVRFEPGEEKSVELIDIGGNRRIFGFNALVDRQADNESKKIALHRAKERGFHGAKSDDNYVKTIKE 238
               SCOP domains d1e9ya2 A:1-105 Urease, gamma-subunit                                                                    d1e9ya1 A:106-238 Urease, beta-subunit                                                                                                SCOP domains
               CATH domains 1e9yA02 A:1-101 Urease, subunit A                                                                    ----1e9yA01 A:106-238 Urease, subunit B                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhh.eeeeeeee..eeeeeeee..............................eeeee......eeee...hhhhh......hhhhhh.eee......eeee....eeeeeeee..................hhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e9y A   1 MKLTPKELDKLMLHYAGELAKKRKEKGIKLNYVEAVALISAHIMEEARAGKKTAAELMQEGRTLLKPDDVMDGVASMIHEVGIEAMFPDGTKLVTVHTPIEANGKLVPGELFLKNEDITINEGKKAVSVKVKNVGDRPVQIGSHFHFFEVNRCLDFDREKTFGKRLDIAAGTAVRFEPGEEKSVELIDIGGNRRIFGFNALVDRQADNESKKIALHRAKERGFHGAKSDDNYVKTIKE 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:569
 aligned with URE1_HELPY | P69996 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:569
                                    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         
           URE1_HELPY     1 MKKISRKEYVSMYGPTTGDKVRLGDTDLIAEVEHDYTIYGEELKFGGGKTLREGMSQSNNPSKEELDLIITNALIVDYTGIYKADIGIKDGKIAGIGKGGNKDMQDGVKNNLSVGPATEALAGEGLIVTAGGIDTHIHFISPQQIPTAFASGVTTMIGGGTGPADGTNATTITPGRRNLKWMLRAAEEYSMNLGFLAKGNASNDASLADQIEAGAIGFKIHEDWGTTPSAINHALDVADKYDVQVAIHTDTLNEAGCVEDTMAAIAGRTMHTFHTEGAGGGHAPDIIKVAGEHNILPASTNPTIPFTVNTEAEHMDMLMVCHHLDKSIKEDVQFADSRIRPQTIAAEDTLHDMGIFSITSSDSQAMGRVGEVITRTWQTADKNKKEFGRLKEEKGDNDNFRIKRYLSKYTINPAIAHGISEYVGSVEVGKVADLVLWSPAFFGVKPNMIIKGGFIALSQMGDANASIPTPQPVYYREMFAHHGKAKYDANITFVSQAAYDKGIKEELGLERQVLPVKNCRNITKKDMQFNDTTAHIEVNPETYHVFVDGKEVTSKPANKVSLAQLFSIF 569
               SCOP domains d1e9yb1 B:1-131,B:432-480 alpha-Subunit of urease                                                                                  d1e9yb2 B:132-431,B:481-569 alpha-subunit of urease, catalytic domain                                                                                                                                                                                                                                       d1e9yb1 B:1-131,B:432-480 alpha-Subunit of ureased1e9yb2 B:132-431,B:481-569 alpha-subunit of urease, catalytic domain                     SCOP domains
               CATH domains -1e9yB01 B:2-130,B:425-482 Urease, subunit C, domain 1                                                                            1e9yB02 B:131-424,B:483-568 Metal-dependent hydrolases                                                                                                                                                                                                                                                1e9yB01 B:2-130,B:425-482 Urease, subunit C, domain 1     1e9yB02 B:131-424,B:483-568 Metal-dependent hydrolases                                - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.........eee......eee....................................eeee.eeeee..eeeeeeeeee..eeeeee...........hhhh......eeee....eeee.eee........hhhhhhhhh.eeeeee.....hhhhhhh...hhhhhhhhhhhhhh....eeee.......hhhhhhhhhhh.......hhhhh.hhhhhhhhhhhhhhh...............hhhhhhhhhh...eee............hhhhhhhh..eee..hhhhh....hhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh.........hhhhhhhhhh..hhhhhhhh................eeee..........eeee..eeeeeee.............eeee.hhhh.hhhhhhheeeehhhhhhhhhhhhh....eeee.......hhhhh........eee......eee...................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------UREASE_1      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UREASE_2         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------UREASE_3  PDB: B:131-569 UniProt: 131-569                                                                                                                                                                                                                                                                                                                                                                                                               PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e9y B   1 MKKISRKEYVSMYGPTTGDKVRLGDTDLIAEVEHDYTIYGEELKFGGGKTLREGMSQSNNPSKEELDLIITNALIVDYTGIYKADIGIKDGKIAGIGKGGNKDMQDGVKNNLSVGPATEALAGEGLIVTAGGIDTHIHFISPQQIPTAFASGVTTMIGGGTGPADGTNATTITPGRRNLKWMLRAAEEYSMNLGFLAKGNASNDASLADQIEAGAIGFkIHEDWGTTPSAINHALDVADKYDVQVAIHTDTLNEAGCVEDTMAAIAGRTMHTFHTEGAGGGHAPDIIKVAGEHNILPASTNPTIPFTVNTEAEHMDMLMVCHHKDKSIKEDVQFADSRIRPQTIAAEDTLHDMGAFSITSSDSQAMGRVGEVITRTWQTADKNKKEFGRLKEEKGDNDNFRIKRYLSKYTINPAIAHGISEYVGSVEVGKVADLVLWSPAFFGVKPNMIIKGGFIALSQMGDANASIPTPQPVYYREMFAHHGKAKYDANITFVSQAAYDKGIKEELGLERQVLPVKNCRNVTKKDMQFNNTTAHIEVNPETYHVFVDGKEVTSKPANKVSLAQLFSIF 569
                                    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         
                                                                                                                                                                                                                                                    219-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 "Pfam Domain" information available for 1E9Y)

Asymmetric Unit(hide GO term definitions)

Chain A (URE23_HELPY | P14916)

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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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 (URE1_HELPY | P69996)

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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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 B:283 - Pro B:284	[ RasMol ]
		Gln B:471 - Pro B:472	[ RasMol ]
		Ile B:304 - Pro B:305	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1e9y
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	URE23_HELPY \| P14916
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UniProtKB/Swiss-Prot
	URE1_HELPY \| P69996	:	1e9z
	URE23_HELPY \| P14916	:	1e9z

1e9z	CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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