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(-) Description

Title :  1.58 A RESOLUTION NATIVE SPOROSARCINA PASTEURII UREASE
 
Authors :  S. Benini, M. Cianci, S. Ciurli
Date :  12 Nov 13  (Deposition) - 27 Aug 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (3x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Benini, M. Cianci, L. Mazzei, S. Ciurli
Fluoride Inhibition Of Sporosarcina Pasteurii Urease: Structure And Thermodynamics.
J. Biol. Inorg. Chem. V. 19 1243 2014
PubMed-ID: 25113581  |  Reference-DOI: 10.1007/S00775-014-1182-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UREASE SUBUNIT GAMMA
    Chains: A
    EC Number: 3.5.1.5
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Strain: DSM33
    Synonym: UREA AMIDOHYDROLASE SUBUNIT GAMMA
 
Molecule 2 - UREASE SUBUNIT ALPHA
    Chains: C
    EC Number: 3.5.1.5
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Strain: DSM33
    Synonym: UREA AMIDOHYDROLASE SUBUNIT ALPHA
 
Molecule 3 - UREASE SUBUNIT BETA
    Chains: B
    EC Number: 3.5.1.5
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Strain: DSM33
    Synonym: UREA AMIDOHYDROLASE SUBUNIT BETA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 22)

Asymmetric Unit (6, 22)
No.NameCountTypeFull Name
1CXM1Mod. Amino AcidN-CARBOXYMETHIONINE
2EDO11Ligand/Ion1,2-ETHANEDIOL
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4NI2Ligand/IonNICKEL (II) ION
5OH1Ligand/IonHYDROXIDE ION
6SO46Ligand/IonSULFATE ION
Biological Unit 1 (4, 57)
No.NameCountTypeFull Name
1CXM3Mod. Amino AcidN-CARBOXYMETHIONINE
2EDO33Ligand/Ion1,2-ETHANEDIOL
3KCX3Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4NI-1Ligand/IonNICKEL (II) ION
5OH-1Ligand/IonHYDROXIDE ION
6SO418Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREKCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , NI C:601 , OH C:1571 , HOH C:2221BINDING SITE FOR RESIDUE NI C 600
02AC2SOFTWAREHIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , NI C:600 , OH C:1571 , HOH C:2196BINDING SITE FOR RESIDUE NI C 601
03AC3SOFTWAREHIS C:137 , KCX C:220 , HIS C:275 , ASP C:363 , NI C:600 , NI C:601 , HOH C:2196 , HOH C:2221 , HOH C:2312BINDING SITE FOR RESIDUE OH C1571
04AC4SOFTWAREASP C:34 , THR C:36 , TYR C:38 , HOH C:2062 , HOH C:2072 , HOH C:2523BINDING SITE FOR RESIDUE EDO C1572
05AC5SOFTWAREGLY A:50 , LYS A:51 , THR A:52 , PHE A:86 , ASP A:88 , HOH A:2120 , VAL C:309 , ASN C:310 , LYS C:559BINDING SITE FOR RESIDUE EDO A1101
06AC6SOFTWAREASP C:286 , ALA C:289 , ILE C:537 , ASP C:538 , ILE C:539 , HOH C:2294 , HOH C:2490BINDING SITE FOR RESIDUE EDO C1573
07AC7SOFTWAREHOH B:2112 , GLY C:46 , HIS C:323 , LEU C:325 , PHE C:335 , HOH C:2256 , HOH C:2526BINDING SITE FOR RESIDUE EDO C1574
08AC8SOFTWAREASP B:101 , HOH B:2170 , HOH B:2203 , PRO C:229 , HOH C:2266 , HOH C:2302BINDING SITE FOR RESIDUE EDO B1127
09AC9SOFTWARETYR C:93 , GLU C:423 , ARG C:513 , ILE C:514 , HOH C:2447 , HOH C:2527BINDING SITE FOR RESIDUE EDO C1575
10BC1SOFTWARETYR C:35 , TYR C:83 , ILE C:97 , GLU C:429 , HOH C:2059 , HOH C:2528BINDING SITE FOR RESIDUE EDO C1576
11BC2SOFTWAREGLY A:27 , LYS A:29 , ASP A:67 , ASP A:68 , HOH A:2045 , HOH A:2058BINDING SITE FOR RESIDUE EDO A1102
12BC3SOFTWAREARG C:62 , PRO C:177 , TRP C:178 , GLU C:181 , HOH C:2227BINDING SITE FOR RESIDUE EDO C1577
13BC4SOFTWAREASN A:4 , ALA A:6 , LYS A:10 , HOH A:2111 , HOH A:2122 , PHE C:568 , PHE C:570 , HOH C:2367BINDING SITE FOR RESIDUE EDO A1103
14BC5SOFTWAREASP C:536 , ASP C:538 , LYS C:547 , VAL C:548 , ASP C:549 , GLY C:550BINDING SITE FOR RESIDUE EDO C1578
15BC6SOFTWARESER C:204 , ILE C:205 , HOH C:2115 , HOH C:2238 , HOH C:2239 , HOH C:2243BINDING SITE FOR RESIDUE SO4 C1579
16BC7SOFTWAREARG B:116 , HOH B:2191BINDING SITE FOR RESIDUE SO4 B1128
17BC8SOFTWAREVAL C:558 , LYS C:559 , GLU C:560 , HOH C:2511 , HOH C:2530 , HOH C:2531BINDING SITE FOR RESIDUE SO4 C1580
18BC9SOFTWARELYS C:511 , HOH C:2532BINDING SITE FOR RESIDUE SO4 C1581
19CC1SOFTWAREHIS C:222 , GLU C:223 , ASP C:224 , HIS C:249 , GLY C:280 , HIS C:323 , ARG C:339 , HOH C:2221 , HOH C:2258 , HOH C:2261 , HOH C:2312BINDING SITE FOR RESIDUE SO4 C1582
20CC2SOFTWAREMET A:70 , GLU A:71 , HOH A:2124 , ARG C:566BINDING SITE FOR RESIDUE SO4 A1104

(-) SS Bonds  (0, 0)

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

(-) 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 4CEU)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UREASE_1PS01120 Urease nickel ligands signature.URE1_SPOPA129-142  1C:130-143
2UREASE_3PS51368 Urease domain profile.URE1_SPOPA131-569  1C:132-570
3UREASE_2PS00145 Urease active site.URE1_SPOPA319-335  1C:320-336
Biological Unit 1 (3, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UREASE_1PS01120 Urease nickel ligands signature.URE1_SPOPA129-142  3C:130-143
2UREASE_3PS51368 Urease domain profile.URE1_SPOPA131-569  3C:132-570
3UREASE_2PS00145 Urease active site.URE1_SPOPA319-335  3C:320-336

(-) Exons   (0, 0)

(no "Exon" information available for 4CEU)

(-) 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_SPOPA | P41022 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           URE3_SPOPA     1 MHLNPAEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS 100
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhh...hhhhhh.eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4ceu A   1 mHLNPAEKEKLQIFLASELLLRRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS 100
                            |       10        20        30        40        50        60        70        80        90       100
                            1-CXM                                                                                               


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with URE2_SPOPA | P41021 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:122
                                    14        24        34        44        54        64        74        84        94       104       114       124  
           URE2_SPOPA     5 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVEVNKELLFDRAEGIGRRLNIPSGTAARFEPGEEMEVELTELGGNREVFGISDLTNGSVDNKELILQRAKELGYKGVE 126
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- 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
                 4ceu B   5 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVEVNKELLFDRAEGIGRRLNIPSGTAARFEPGEEMEVELTELGGNREVFGISDLTNGSVDNKELILQRAKELGYKGVE 126
                                    14        24        34        44        54        64        74        84        94       104       114       124  


Chain C from PDB  Type:PROTEIN  Length:570
 aligned with URE1_SPOPA | P41020 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:570
                                                        29                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                      28 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569
           URE1_SPOPA     1 MKINRQQYAESYGPTVGDRVRLADTDLG-EVEKDYYYLGDEVNFGGGKVLREGMGENGTYTRTENVLDLLLTNALILDYTGIYKADIGVKDGYIVGIGKGGNPDIMDGVTPNMIVGTATEVIAAEGKIVTAGGIDTHVHFINPDQVDVALANGITTLFGGGTGPAEGSKATTVTPGPWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGAAGLKIHEDWGATPASIDRSLTVADEADVQVAIHSDTLNEAGFLEDTVRAINGRVIHSFHVEGAGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIRPETIAAEDILHDLGIISMMSTDALAMGRAGEMVLRTWQTADKMKKQRGPLAEEKNGSDNFRLKRYVSKYTINPAIAQGMAHEVGSIEEGKFADLVLWEPKFFGVKADRVIKGGIIAYAQIGDPSASIPTPQPVMGRRMYGTVGDLIHDTNITFMSKSSIQQGVPAKLGLKRRIGTVKNCRNIGKKDMKWNDVTTDIDINPETYEVKVDGEVLTCEPVKELPMAQRYFLF 569
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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...........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh................eeeehhhhh.....eeee..eeeeeee.............eeee.hhhhhhhhhhh.eeeehhhhhhhhhhhhhh...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: C:132-570 UniProt: 131-569                                                                                                                                                                                                                                                                                                                                                                                                               PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ceu 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)
  - → 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  (0, 0)

(no "SCOP Domain" information available for 4CEU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (URE3_SPOPA | P41022)
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: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_SPOPA | P41021)
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_SPOPA | P41020)
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: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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  URE1_SPOPA | P41020
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  URE2_SPOPA | P41021
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  URE3_SPOPA | P41022
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4cex 1.58 A RESOLUTION FLUORIDE INHIBITED SPOROSARCINA PASTEURII UREASE