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(-) Description

Title :  FINAL UREASE STRUCTURE FOR RADIATION DAMAGE EXPERIMENT AT 300 K
 
Authors :  M. Warkentin, R. Badeau, J. B. Hopkins, R. E. Thorne
Date :  17 Apr 12  (Deposition) - 29 Aug 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (3x)
Keywords :  Alpha-Beta Barrel, Nickel Metalloenzyme, Hydrolase, Radiation Damage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Warkentin, R. Badeau, J. B. Hopkins, R. E. Thorne
Spatial Distribution Of Radiation Damage To Crystalline Proteins At 25-300 K.
Acta Crystallogr. , Sect. D V. 68 1108 2012
PubMed-ID: 22948911  |  Reference-DOI: 10.1107/S0907444912021361

(-) Compounds

Molecule 1 - UREASE SUBUNIT ALPHA
    Chains: C
    EC Number: 3.5.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UREC
    Organism Scientific: ENTEROBACTER AEROGENES
    Organism Taxid: 548
    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
    Gene: UREB
    Organism Common: AEROBACTER AEROGENES
    Organism Scientific: ENTEROBACTER AEROGENES
    Organism Taxid: 548
    Synonym: UREA AMIDOHYDROLASE SUBUNIT BETA
 
Molecule 3 - UREASE SUBUNIT GAMMA
    Chains: A
    EC Number: 3.5.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UREA
    Organism Scientific: ENTEROBACTER AEROGENES
    Organism Taxid: 548
    Synonym: UREA AMIDOHYDROLASE SUBUNIT GAMMA

 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  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREKCX C:1217 , HIS C:1219 , HIS C:1246 , HIS C:1272 , GLY C:1277 , NI C:1602 , HOH C:1702BINDING SITE FOR RESIDUE NI C 1601
2AC2SOFTWAREHIS C:1134 , HIS C:1136 , KCX C:1217 , ASP C:1360 , NI C:1601 , HOH C:1703BINDING SITE FOR RESIDUE NI C 1602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EPE)

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EPE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EPE)

(-) Exons   (0, 0)

(no "Exon" information available for 4EPE)

(-) 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
                                                                                                                                     
               SCOP domains d4epea_ A: Urease, gamma-subunit                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhh..hhhhhh.eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                4epe A 3001 MELTPREKDKLLLFTAALVAERRLARGLKLNYPESVALISAFIMEGARDGKSVASLMEEGRHVLTREQVMEGVPEMIPDIQVEATFPDGSKLVTVHNPII 3100
                                  3010      3020      3030      3040      3050      3060      3070      3080      3090      3100


Chain B from PDB  Type:PROTEIN  Length:101
                                                                                                                                      
               SCOP domains d4epeb_ B: Urease, beta-subunit                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- 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
                4epe B 2001 MIPGEYHVKPGQIALNTGRATCRVVVENHGDRPIQVGSHYHFAEVNPALKFDRQQAAGYRLNIPAGTAVRFEPGQKREVELVAFAGHRAVFGFRGEVMGPL 2101
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100 


Chain C from PDB  Type:PROTEIN  Length:566
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4epec1 C:1002-1129,C:1423-1475 alpha-Subunit of urease                                                                         d4epec2 C:1130-1422,C:1476-1567 alpha-subunit of urease, catalytic domain                                                                                                                                                                                                                            d4epec1 C:1002-1129,C:1423-1475                      d4epec2 C:1130-1422,C:1476-1567 alpha-subunit of urease, catalytic domain                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhh.....eee......eee..ee.........................hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeee.ee.........ee.....eeee....eeee.eeeeeee....hhhhhhhhhheeeeeee....hhhhhhh...hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhh..eeeee.hhh.hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhh...eee............hhhhhhhh..eeeeee........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....eee..........hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.hhhhhhhh................eeeehhhhh.....eeee..eeeeeee.............eeee.hhhhhhhhhhhheeeehhhhhhhhhhhhhh...eeee.......hhhhh........eee......eee..ee.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4epe C 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
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EPE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EPE)

(-) Gene Ontology  (10, 21)

Asymmetric Unit(hide GO term definitions)

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  URE1_ENTAE | P18314
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  URE2_ENTAE | P18315
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 Related Entries

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

UniProtKB/Swiss-Prot
        URE1_ENTAE | P18314: 1a5k 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 2kau 4ep8 4epb 4epd
        URE2_ENTAE | P18315: 1a5k 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 2kau 4ep8 4epb 4epd
        URE3_ENTAE | P18316: 1a5k 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 2kau 4ep8 4epb 4epd

(-) Related Entries Specified in the PDB File

4ep8 4epb 4epd