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(-) Description

Title :  STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION
 
Authors :  S. Benini, W. R. Rypniewski, K. S. Wilson, S. Ciurli, S. Mangani
Date :  25 Feb 99  (Deposition) - 06 Mar 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (3x)
Keywords :  Urease, Bacillus Pasteurii, Nickel, Acetohydroxamic Acid, Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Benini, W. R. Rypniewski, K. S. Wilson, S. Miletti, S. Ciurli, S. Mangani
The Complex Of Bacillus Pasteurii Urease With Acetohydroxamate Anion From X-Ray Data At 1. 55 A Resolution
J. Biol. Inorg. Chem. V. 5 110 2000
PubMed-ID: 10766443  |  Reference-DOI: 10.1007/S007750050014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (UREASE (CHAIN A))
    Cellular Location: CYTOPLASM
    Chains: A
    EC Number: 3.5.1.5
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Strain: DSM 33
    Synonym: UREA AMINOHYDROLASE
 
Molecule 2 - PROTEIN (UREASE (CHAIN B))
    Cellular Location: CYTOPLASM
    Chains: B
    EC Number: 3.5.1.5
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Strain: DSM 33
    Synonym: UREA AMINOHYDROLASE
 
Molecule 3 - PROTEIN (UREASE (CHAIN C))
    Cellular Location: CYTOPLASM
    Chains: C
    EC Number: 3.5.1.5
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Strain: DSM 33
    Synonym: UREA AMINOHYDROLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (3x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HAE1Ligand/IonACETOHYDROXAMIC ACID
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HAE1Ligand/IonACETOHYDROXAMIC ACID
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2HAE3Ligand/IonACETOHYDROXAMIC ACID
3KCX3Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREKCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , NI C:799 , HAE C:800BINDING SITE FOR RESIDUE NI C 798
2AC2SOFTWAREHIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , NI C:798 , HAE C:800BINDING SITE FOR RESIDUE NI C 799
3AC3SOFTWAREHIS C:137 , ALA C:170 , KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , ASP C:363 , NI C:798 , NI C:799BINDING SITE FOR RESIDUE HAE C 800
4CATAUTHORHIS C:137 , HIS C:139 , KCX C:220 , HIS C:249 , HIS C:275 , ASP C:363THE DINUCLEAR NI2+ METALLOCENTER IS INHIBITED BY A MOLECULE OF ACETOHYDROXAMIC ACID

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala C:284 -Pro C:285
2Arg C:305 -Pro C:306
3Gln C:472 -Pro C:473

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UBP)

(-) 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:101
                                                                                                                                     
               SCOP domains d4ubpa_ A: Urease, gamma-subunit                                                                      SCOP domains
               CATH domains -4ubpA00 A:1-100 Urease, subunit A                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhh..hhhhhh.eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4ubp A   0 xMHLNPAEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS 100
                            |        9        19        29        39        49        59        69        79        89        99 
                            |                                                                                                    
                            0-ACE                                                                                                


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4ubpb_ B: Urease, beta-subunit                                                                                            SCOP domains
               CATH domains 4ubpB00 B:5-126 Urease, subunit B                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....eee......eeeeeeee.....eeee...hhhhh...ee.hhhhhh.eee......eeee....eeeeeeee.....ee........ee..hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ubp B   5 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVEVNKELLFDRAEGIGRRLNIPSGTAARFEPGEEMEVELTELGGNREVFGISDLTNGSVDNKELILQRAKELGYKGVE 126
                                    14        24        34        44        54        64        74        84        94       104       114       124  


Chain C from PDB  Type:PROTEIN  Length:570
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4ubpc1 C:1-131,C:435-483 alpha-Subunit of urease                                                                                  d4ubpc2 C:132-434,C:484-570 alpha-subunit of urease, catalytic domain                                                                                                                                                                                                                                          d4ubpc1 C:1-131,C:435-483 alpha-Subunit of ureased4ubpc2 C:132-434,C:484-570 alpha-subunit of urease, catalytic domain                   SCOP domains
               CATH domains 4ubpC01 C:1-131,C:426-483 Urease, subunit C, domain 1                                                                              4ubpC02 C:132-425,C:484-569 Metal-dependent hydrolases                                                                                                                                                                                                                                                4ubpC01 C:1-131,C:426-483 Urease, subunit C, domain 1     4ubpC02 C:132-425,C:484-569 Metal-dependent hydrolases                                - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhh.....eee......eee......................................eeeeeeeeee..eeeeeeeeee..eeeeee.....................eeee....eeee.eeeeeee....hhhhhhhhh.eeeeeee....hhhhhhh...hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhh..eeeee.hhh.hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhh...eee............hhhhhhhh..eee...........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.hhhhhhhh................eeeehhhhh.....eeee..eeeeeee.............eeee.hhhhhhhhhhh.eeeehhhhhhhhhhhhhh...eeee.......hhhhh.........ee......eee..ee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ubp C   1 MKINRQQYAESYGPTVGDEVRLADTDLWIEVEKDYTTYGDEVNFGGGKVLREGMGENGTYTRTENVLDLLLTNALILDYTGIYKADIGVKDGYIVGIGKGGNPDIMDGVTPNMIVGTATEVIAAEGKIVTAGGIDTHVHFINPDQVDVALANGITTLFGGGTGPAEGSKATTVTPGPWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGAAGLkIHEDWGATPASIDRSLTVADEADVQVAIHSDTLNEAGFLEDTLRAINGRVIHSFHVEGAGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIRPETIAAEDILHDLGIISMMSTDALAMGRAGEMVLRTWQTADKMKKQRGPLAEEKNGSDNFRLKRYVSKYTINPAIAQGIAHEVGSIEEGKFADLVLWEPKFFGVKADRVIKGGIIAYAQIGDPSASIPTPQPVMGRRMYGTVGDLIHDTNITFMSKSSIQQGVPAKLGLKRRIGTVKNCRNIGKKDMKWNDVTTDIDINPETYEVKVDGEVLTCEPVKELPMAQRYFLF 570
                                    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       570
                                                                                                                                                                                                                                                     220-KCX
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 19)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        URE1_SPOPA | P41020: 1ie7 1s3t 1ubp 2ubp 3ubp 4ac7 4ceu 4cex 5a6t 5fsd 5fse
        URE2_SPOPA | P41021: 1ie7 1s3t 1ubp 2ubp 3ubp 4ac7 4ceu 4cex 5a6t 5fsd 5fse 5g4h
        URE3_SPOPA | P41022: 1ie7 1s3t 1ubp 2ubp 3ubp 4ac7 4ceu 4cex 5a6t 5fsd 5fse 5g4h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4UBP)