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(-) Description

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)

(-) Compounds

Molecule 1 - UREASE (GAMMA CHAIN)
    ChainsA
    EC Number3.5.1.5
    EngineeredYES
    Expression SystemKLEBSIELLA AEROGENES
    Expression System PlasmidPKAU19
    Expression System StrainCG253
    Expression System Taxid28451
    GeneUREC
    OrganBEAN
    Organism ScientificKLEBSIELLA AEROGENES
    Organism Taxid28451
 
Molecule 2 - UREASE (BETA CHAIN)
    ChainsB
    EC Number3.5.1.5
    EngineeredYES
    Expression SystemKLEBSIELLA AEROGENES
    Expression System PlasmidPKAU19
    Expression System StrainCG253
    Expression System Taxid28451
    GeneUREB
    OrganBEAN
    Organism ScientificKLEBSIELLA AEROGENES
    Organism Taxid28451
 
Molecule 3 - UREASE (ALPHA CHAIN)
    ChainsC
    EC Number3.5.1.5
    EngineeredYES
    Expression SystemKLEBSIELLA AEROGENES
    Expression System PlasmidPKAU19
    Expression System StrainCG253
    Expression System Taxid28451
    GeneUREA
    OrganBEAN
    Organism ScientificKLEBSIELLA AEROGENES
    Organism Taxid28451

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (3x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1KCX3Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREKCX C:217 , HIS C:246 , HIS C:272 , GLY C:277 , NI C:775BINDING SITE FOR RESIDUE NI C 774
2AC2SOFTWAREHIS C:134 , HIS C:136 , KCX C:217 , ASP C:360 , NI C:774BINDING SITE FOR RESIDUE NI C 775
3ACCAUTHORHIS C:219 , HIS C:320RESIDUES IMPLICATED IN CATALYSIS

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UREASE_1PS01120 Urease nickel ligands signature.URE1_ENTAE127-140  1C:127-140
2UREASE_3PS51368 Urease domain profile.URE1_ENTAE129-567  1C:129-567
3UREASE_2PS00145 Urease active site.URE1_ENTAE317-333  1C:317-333
Biological Unit 1 (3, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UREASE_1PS01120 Urease nickel ligands signature.URE1_ENTAE127-140  3C:127-140
2UREASE_3PS51368 Urease domain profile.URE1_ENTAE129-567  3C:129-567
3UREASE_2PS00145 Urease active site.URE1_ENTAE317-333  3C:317-333

(-) Exons   (0, 0)

(no "Exon" information available for 2KAU)

(-) Sequences/Alignments

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 '|'

 Classification and Annotation

(-) SCOP Domains  (4, 4)

Asymmetric Unit

(-) CATH Domains  (4, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2KAU)

(-) Gene Ontology  (10, 21)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        URE1_ENTAE | P183141a5k 1a5l 1a5m 1a5n 1a5o 1ef2 1ejr 1ejs 1ejt 1eju 1ejv 1ejw 1ejx 1fwa 1fwb 1fwc 1fwd 1fwe 1fwf 1fwg 1fwh 1fwi 1fwj 1kra 1krb 1krc 4ep8 4epb 4epd 4epe
        URE2_ENTAE | P183151a5k 1a5l 1a5m 1a5n 1a5o 1ef2 1ejr 1ejs 1ejt 1eju 1ejv 1ejw 1ejx 1fwa 1fwb 1fwc 1fwd 1fwe 1fwf 1fwg 1fwh 1fwi 1fwj 1kra 1krb 1krc 4ep8 4epb 4epd 4epe
        URE3_ENTAE | P183161a5k 1a5l 1a5m 1a5n 1a5o 1ef2 1ejr 1ejs 1ejt 1eju 1ejv 1ejw 1ejx 1fwa 1fwb 1fwc 1fwd 1fwe 1fwf 1fwg 1fwh 1fwi 1fwj 1kra 1krb 1krc 4ep8 4epb 4epd 4epe

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2KAU)