2KAU - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF UREASE FROM KLEBSIELLA AEROGENES AT 2.2 ANGSTROMS RESOLUTION

Authors :   E. Jabri, M. B. Carr, R. P. Hausinger, P. A. Karplus

Date :   16 Feb 95 (Deposition) - 10 Jul 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Nickel Metalloenzyme, Hydrolase (Urea Amido), Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Jabri, M. B. Carr, R. P. Hausinger, P. A. Karplus
The Crystal Structure Of Urease From Klebsiella Aerogenes.
Science V. 268 998 1995
PubMed-ID: 7754395
(for further references see the PDB file header)

Molecule 1 - UREASE (GAMMA CHAIN)
	Chains	:	A
	EC Number	:	3.5.1.5
	Engineered	:	YES
	Expression System	:	KLEBSIELLA AEROGENES
	Expression System Plasmid	:	PKAU19
	Expression System Strain	:	CG253
	Expression System Taxid	:	28451
	Gene	:	UREC
	Organ	:	BEAN
	Organism Scientific	:	KLEBSIELLA AEROGENES
	Organism Taxid	:	28451

Molecule 2 - UREASE (BETA CHAIN)
	Chains	:	B
	EC Number	:	3.5.1.5
	Engineered	:	YES
	Expression System	:	KLEBSIELLA AEROGENES
	Expression System Plasmid	:	PKAU19
	Expression System Strain	:	CG253
	Expression System Taxid	:	28451
	Gene	:	UREB
	Organ	:	BEAN
	Organism Scientific	:	KLEBSIELLA AEROGENES
	Organism Taxid	:	28451

Molecule 3 - UREASE (ALPHA CHAIN)
	Chains	:	C
	EC Number	:	3.5.1.5
	Engineered	:	YES
	Expression System	:	KLEBSIELLA AEROGENES
	Expression System Plasmid	:	PKAU19
	Expression System Strain	:	CG253
	Expression System Taxid	:	28451
	Gene	:	UREA
	Organ	:	BEAN
	Organism Scientific	:	KLEBSIELLA AEROGENES
	Organism Taxid	:	28451

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

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

Biological Unit 1 (1, 3)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	KCX C:217 , HIS C:246 , HIS C:272 , GLY C:277 , NI C:775	BINDING SITE FOR RESIDUE NI C 774
2	AC2	SOFTWARE	HIS C:134 , HIS C:136 , KCX C:217 , ASP C:360 , NI C:774	BINDING SITE FOR RESIDUE NI C 775
3	ACC	AUTHOR	HIS C:219 , HIS C:320	RESIDUES IMPLICATED IN CATALYSIS

(no "SS Bond" information available for 2KAU)

Asymmetric Unit

No.	Residues
1	Ala C:281	-	Pro C:282
2	Leu C:302	-	Pro C:303
3	Gln C:469	-	Pro C:470

(no "SAP(SNP)/Variant" information available for 2KAU)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UREASE_1	PS01120	Urease nickel ligands signature.	URE1_ENTAE	127-140	1	C:127-140
2	UREASE_3	PS51368	Urease domain profile.	URE1_ENTAE	129-567	1	C:129-567
3	UREASE_2	PS00145	Urease active site.	URE1_ENTAE	317-333	1	C:317-333

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_ENTAE	127-140	3	C:127-140
2	UREASE_3	PS51368	Urease domain profile.	URE1_ENTAE	129-567	3	C:129-567
3	UREASE_2	PS00145	Urease active site.	URE1_ENTAE	317-333	3	C:317-333

(no "Exon" information available for 2KAU)

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_ENTAE | P18316 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           URE3_ENTAE     1 MELTPREKDKLLLFTAALVAERRLARGLKLNYPESVALISAFIMEGARDGKSVASLMEEGRHVLTREQVMEGVPEMIPDIQVEATFPDGSKLVTVHNPII 100
               SCOP domains d2kaua_ A: Urease, gamma-subunit                                                                     SCOP domains
               CATH domains 2kauA00 A:1-100 Urease, subunit A                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhh....hhhh..eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2kau A   1 MELTPREKDKLLLFTAALVAERRLARGLKLNYPESVALISAFIMEGARDGKSVASLMEEGRHVLTREQVMEGVPEMIPDIQVEATFPDGSKLVTVHNPII 100
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with URE2_ENTAE | P18315 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
           URE2_ENTAE     1 MIPGEYHVKPGQIALNTGRATCRVVVENHGDRPIQVGSHYHFAEVNPALKFDRQQAAGYRLNIPAGTAVRFEPGQKREVELVAFAGHRAVFGFRGEVMGPL 101
               SCOP domains d2kaub_ B: Urease, beta-subunit                                                                       SCOP domains
               CATH domains 2kauB00 B:1-101 Urease, subunit B                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee......eeeeeee......eeee....hhh..............eee......eeee....eeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2kau B   1 MIPGEYHVKPGQIALNTGRATCRVVVENHGDRPIQVGSHYHFAEVNPALKFDRQQAAGYRLNIPAGTAVRFEPGQKREVELVAFAGHRAVFGFRGEVMGPL 101
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:566
 aligned with URE1_ENTAE | P18314 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:566
                                    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       461       471       481       491       501       511       521       531       541       551       561      
           URE1_ENTAE     2 SNISRQAYADMFGPTVGDKVRLADTELWIEVEDDLTTYGEEVKFGGGKVIRDGMGQGQMLAADCVDLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNPDIQPNVTIPIGAATEVIAAEGKIVTAGGIDTHIHWICPQQAEEALVSGVTTMVGGGTGPAAGTHATTCTPGPWYISRMLQAADSLPVNIGLLGKGNVSQPDALREQVAAGVIGLKIHEDWGATPAAIDCALTVADEMDIQVALHSDTLNESGFVEDTLAAIGGRTIHTFHTEGAGGGHAPDIITACAHPNILPSSTNPTLPYTLNTIDEHLDMLMVCHHLDPDIAEDVAFAESRIRRETIAAEDVLHDLGAFSLTSSDSQAMGRVGEVILRTWQVAHRMKVQRGALAEETGDNDNFRVKRYIAKYTINPALTHGIAHEVGSIEVGKLADLVVWSPAFFGVKPATVIKGGMIAIAPMGDINASIPTPQPVHYRPMFGALGSARHHCRLTFLSQAAAANGVAERLNLRSAIAVVKGCRTVQKADMVHNSLQPNITVDAQTYEVRVDGELITSEPADVLPMAQRYFLF 567
               SCOP domains d2kauc1 C:2-129,C:423-475 alpha-Subunit of urease                                                                               d2kauc2 C:130-422,C:476-567 alpha-subunit of urease, catalytic domain                                                                                                                                                                                                                                d2kauc1 C:2-129,C:423-475 alpha-Subunit of urease    d2kauc2 C:130-422,C:476-567 alpha-subunit of urease, catalytic domain                        SCOP domains
               CATH domains 2kauC01 C:2-128,C:423-480 Urease, subunit C, domain 1                                                                          2kauC02 C:129-422,C:481-567 Metal-dependent hydrolases                                                                                                                                                                                                                                                2kauC01 C:2-128,C:423-480 Urease, subunit C, domain 1     2kauC02 C:129-422,C:481-567 Metal-dependent hydrolases                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhh......eee......eee..............................hhh...eeee.eeeee..eeeeeeeeee..eeeeee...................eeee...eeeee.eee.......hhhhhhhhhh.eeeeee......hhhhh.....hhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhh...eeeeehhh...hhhhhhhhhhhhhh..eeeee.........hhhhhhhh....eee.............hhhhhh...eee............hhhhhhhhhhh........hhhh..hhhh..hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh...........hhhhhhhhhhh.hhhhhh.................eeeeehhh......eeee..eeeeeee.............eeee.hhh.hhhhhhh.eeee.hhhhh..hhhh.....eeee........hhh.........eee......eee...................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------UREASE_1      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UREASE_2         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------UREASE_3  PDB: C:129-567 UniProt: 129-567                                                                                                                                                                                                                                                                                                                                                                                                               PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kau C   2 SNISRQAYADMFGPTVGDKVRLADTELWIEVEDDLTTYGEEVKFGGGKVIRDGMGQGQMLAADCVDLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNPDIQPNVTIPIGAATEVIAAEGKIVTAGGIDTHIHWICPQQAEEALVSGVTTMVGGGTGPAAGTHATTCTPGPWYISRMLQAADSLPVNIGLLGKGNVSQPDALREQVAAGVIGLkIHEDWGATPAAIDCALTVADEMDIQVALHSDTLNESGFVEDTLAAIGGRTIHTFHTEGAGGGHAPDIITACAHPNILPSSTNPTLPYTLNTIDEHLDMLMVCHHLDPDIAEDVAFAESRIRRETIAAEDVLHDLGAFSLTSSDSQAMGRVGEVILRTWQVAHRMKVQRGALAEETGDNDNFRVKRYIAKYTINPALTHGIAHEVGSIEVGKLADLVVWSPAFFGVKPATVIKGGMIAIAPMGDINASIPTPQPVHYRPMFGALGSARHHCRLTFLSQAAAANGVAERLNLRSAIAVVKGCRTVQKADMVHNSLQPNITVDAQTYEVRVDGELITSEPADVLPMAQRYFLF 567
                                    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       461       471       481       491       501       511       521       531       541       551       561      
                                                                                                                                                                                                                                                 217-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 2KAU)

Asymmetric Unit(hide GO term definitions)

Chain A (URE3_ENTAE | P18316)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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_ENTAE | P18315)

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_ENTAE | P18314)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:281 - Pro C:282	[ RasMol ]
		Gln C:469 - Pro C:470	[ RasMol ]
		Leu C:302 - Pro C:303	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2kau
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	URE2_ENTAE \| P18315
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(no "Related Entries Specified in the PDB File" available for 2KAU)

Description

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

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Cis Peptide Bonds (3, 3)

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