1EF2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF MANGANESE-SUBSTITUTED KLEBSIELLA AEROGENES UREASE

Authors :   K. Yamaguchi, N. J. Cosper, C. Stalhandske, R. A. Scott, M. A. Pearson, P. A. Karplus, R. P. Hausinger

Date :   05 Feb 00 (Deposition) - 09 Mar 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Alpha-Beta Barrel, Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Yamaguchi, N. J. Cosper, C. Stalhandske, R. A. Scott, M. A. Pearson, P. A. Karplus, R. P. Hausinger
Characterization Of Metal-Substituted Klebsiella Aerogenes Urease.
J. Biol. Inorg. Chem. V. 4 468 1999
PubMed-ID: 10555581 | Reference-DOI: 10.1007/S007750050333

Molecule 1 - UREASE ALPHA SUBUNIT
	Chains	:	A
	EC Number	:	3.5.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	KLEBSIELLA AEROGENES
	Organism Taxid	:	28451

Molecule 2 - UREASE BETA SUBUNIT
	Chains	:	B
	EC Number	:	3.5.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	KLEBSIELLA AEROGENES
	Organism Taxid	:	28451

Molecule 3 - UREASE GAMMA SUBUNIT
	Chains	:	C
	EC Number	:	3.5.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	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	MN	2	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (1, 3)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:500 , HOH A:501 , KCX A:1217 , HIS A:1219 , HIS A:1246 , HIS A:1272 , GLY A:1277 , MN A:4775	BINDING SITE FOR RESIDUE MN A 4774
2	AC2	SOFTWARE	HOH A:500 , HOH A:502 , HIS A:1134 , HIS A:1136 , KCX A:1217 , ASP A:1360 , MN A:4774	BINDING SITE FOR RESIDUE MN A 4775

(no "SS Bond" information available for 1EF2)

Asymmetric Unit

No.	Residues
1	Ala A:1281	-	Pro A:1282
2	Leu A:1302	-	Pro A:1303
3	Gln A:1469	-	Pro A:1470

(no "SAP(SNP)/Variant" information available for 1EF2)

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	A:1127-1140
2	UREASE_3	PS51368	Urease domain profile.	URE1_ENTAE	129-567	1	A:1129-1567
3	UREASE_2	PS00145	Urease active site.	URE1_ENTAE	317-333	1	A:1317-1333

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	A:1127-1140
2	UREASE_3	PS51368	Urease domain profile.	URE1_ENTAE	129-567	3	A:1129-1567
3	UREASE_2	PS00145	Urease active site.	URE1_ENTAE	317-333	3	A:1317-1333

(no "Exon" information available for 1EF2)

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: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 d1ef2a1 A:1002-1129,A:1423-1475 alpha-Subunit of urease                                                                         d1ef2a2 A:1130-1422,A:1476-1567 alpha-subunit of urease, catalytic domain                                                                                                                                                                                                                            d1ef2a1 A:1002-1129,A:1423-1475                      d1ef2a2 A:1130-1422,A:1476-1567 alpha-subunit of urease, catalytic domain                    SCOP domains
               CATH domains 1ef2A01 A:1002-1128,A:1423-1480 Urease, subunit C, domain 1                                                                    1ef2A02 A:1129-1422,A:1481-1566 Metal-dependent hydrolases                                                                                                                                                                                                                                            1ef2A01 A:1002-1128,A:1423-1480                           1ef2A02 A:1129-1422,A:1481-1566 Metal-dependent hydrolases                            - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhh.....eee......eee..ee.........................hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeee.ee.........ee.....eeee....eeee.eeeeeee....hhhhhhhhhheeeeeee....hhhhhhh...hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhh..eeeee.hhh.hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhh...eee............hhhhhhhh..eeeeee.hhh....hhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhh....eee..........hhhhhhhhhhhhhhhhhh.........hhhhhhhhhh..hhhhhhhh................eeeehhhhh.....eeee..eeeeeee.............eeee.hhhhhhhhhhhheeeehhhhhhhhhhhhh....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: A:1129-1567 UniProt: 129-567                                                                                                                                                                                                                                                                                                                                                                                                             PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ef2 A 1002 SNISRQAYADMFGPTVGDKVRLADTELWIEVEDDLTTYGEEVKFGGGKVIRDGMGQGQMLAADCVDLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNPDIQPNVTIPIGAATEVIAAEGKIVTAGGIDTHIHWICPQQAEEALVSGVTTMVGGGTGPAAGTHATTCTPGPWYISRMLQAADSLPVNIGLLGKGNVSQPDALREQVAAGVIGLkIHEDWGATPAAIDCALTVADEMDIQVALHSDTLNESGFVEDTLAAIGGRTIHTFHTEGAGGGHAPDIITACAHPNILPSSTNPTLPYTLNTIDEHLDMLMVCHHLDPDIAEDVAFAESRIRRETIAAEDVLHDLGAFSLTSSDSQAMGRVGEVILRTWQVAHRMKVQRGALAEETGDNDNFRVKRYIAKYTINPALTHGIAHEVGSIEVGKLADLVVWSPAFFGVKPATVIKGGMIAIAPMGDINASIPTPQPVHYRPMFGALGSARHHCRLTFLSQAAAANGVAERLNLRSAIAVVKGCRTVQKADMVHNSLQPNITVDAQTYEVRVDGELITSEPADVLPMAQRYFLF 1567
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211     |1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491      1501      1511      1521      1531      1541      1551      1561      
                                                                                                                                                                                                                                                1217-KCX

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 d1ef2b_ B: Urease, beta-subunit                                                                       SCOP domains
               CATH domains 1ef2B00 B:2001-2101 Urease, subunit B                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....eee......eeeeeeee.....eeee...hhhhh...ee........eee......eeee....eeeeeeee.....ee........ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                1ef2 B 2001 MIPGEYHVKPGQIALNTGRATCRVVVENHGDRPIQVGSHYHFAEVNPALKFDRQQAAGYRLNIPAGTAVRFEPGQKREVELVAFAGHRAVFGFRGEVMGPL 2101
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100

Chain C 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 d1ef2c_ C: Urease, gamma-subunit                                                                     SCOP domains
               CATH domains 1ef2C00 C:3001-3100 Urease, subunit A                                                                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
                1ef2 C 3001 MELTPREKDKLLLFTAALVAERRLARGLKLNYPESVALISAFIMEGARDGKSVASLMEEGRHVLTREQVMEGVPEMIPDIQVEATFPDGSKLVTVHNPII 3100
                                  3010      3020      3030      3040      3050      3060      3070      3080      3090      3100

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 1EF2)

Asymmetric Unit(hide GO term definitions)

Chain A (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.

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 (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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:1281 - Pro A:1282	[ RasMol ]
		Gln A:1469 - Pro A:1470	[ RasMol ]
		Leu A:1302 - Pro A:1303	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1ef2
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	URE2_ENTAE \| P18315
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	URE3_ENTAE \| P18316
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1fwj	WILD-TYPE KLEBSIELLA AEROGENES UREASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

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SCOP Domains (4, 4)

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