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(-) Description

Title :  1.75 A RESOLUTION 2,5-DIHYDROXYBENZENSULFONATE INHIBITED SPOROSARCINA PASTEURII UREASE
 
Authors :  L. Mazzei, M. Cianci, F. Musiani, S. Ciurli
Date :  04 Jan 16  (Deposition) - 23 Mar 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (3x)
Keywords :  Hydrolase, Urease, Sporosarcina Pasteurii, Nickel, Metalloenzyme, 2, 5-Dihydroxybenzensulfonate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Mazzei, M. Cianci, F. Musiani, S. Ciurli
Inactivation Of Urease By 1, 4-Benzoquinone: Chemistry At The Protein Surface.
Dalton Trans V. 45 5455 2016
PubMed-ID: 26961812  |  Reference-DOI: 10.1039/C6DT00652C

(-) Compounds

Molecule 1 - UREASE SUBUNIT GAMMA
    Atcc: 11859
    Chains: A
    EC Number: 3.5.1.5
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Synonym: UREA AMIDOHYDROLASE SUBUNIT GAMMA
    Variant: DSM 33
 
Molecule 2 - UREASE SUBUNIT BETA
    Atcc: 11859
    Chains: B
    EC Number: 3.5.1.5
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Synonym: UREA AMIDOHYDROLASE SUBUNIT BETA
    Variant: DSM 33
 
Molecule 3 - UREASE SUBUNIT ALPHA
    Atcc: 11859
    Chains: C
    EC Number: 3.5.1.5
    Organism Scientific: SPOROSARCINA PASTEURII
    Organism Taxid: 1474
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Synonym: UREA AMIDOHYDROLASE SUBUNIT ALPHA
    Variant: DSM 33

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 29)

Asymmetric Unit (7, 29)
No.NameCountTypeFull Name
1CXM1Mod. Amino AcidN-CARBOXYMETHIONINE
2DBX2Ligand/Ion2,5-DIHYDROXYBENZENESULFONIC ACID
3EDO16Ligand/Ion1,2-ETHANEDIOL
4KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
5NI2Ligand/IonNICKEL (II) ION
6OH1Ligand/IonHYDROXIDE ION
7SO46Ligand/IonSULFATE ION
Biological Unit 1 (5, 78)
No.NameCountTypeFull Name
1CXM3Mod. Amino AcidN-CARBOXYMETHIONINE
2DBX6Ligand/Ion2,5-DIHYDROXYBENZENESULFONIC ACID
3EDO48Ligand/Ion1,2-ETHANEDIOL
4KCX3Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
5NI-1Ligand/IonNICKEL (II) ION
6OH-1Ligand/IonHYDROXIDE ION
7SO418Ligand/IonSULFATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREKCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , NI C:601 , OH C:1584 , HOH C:2165BINDING SITE FOR RESIDUE NI C 600
02AC2SOFTWAREHIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , NI C:600 , OH C:1584 , HOH C:2143BINDING SITE FOR RESIDUE NI C 601
03AC3SOFTWAREASP C:34 , THR C:36 , TYR C:38 , HOH C:2040 , HOH C:2054 , HOH C:2406BINDING SITE FOR RESIDUE EDO C1572
04AC4SOFTWARETYR C:60 , ASN C:65 , ILE C:114 , SO4 C:1585 , HOH C:2128BINDING SITE FOR RESIDUE EDO C1573
05AC5SOFTWAREHIS C:422 , GLY C:430 , GLN C:501 , HOH C:2317BINDING SITE FOR RESIDUE EDO C1574
06AC6SOFTWARETYR C:93 , GLU C:423 , GLN C:501 , ARG C:513 , ILE C:514 , HOH C:2409BINDING SITE FOR RESIDUE EDO C1575
07AC7SOFTWAREPRO C:143 , GLY C:189 , ARG C:478 , HOH C:2410BINDING SITE FOR RESIDUE EDO C1576
08AC8SOFTWARELYS A:10 , THR A:85 , THR A:90 , PHE C:570 , HOH C:2411BINDING SITE FOR RESIDUE EDO C1577
09AC9SOFTWAREASP B:101 , HOH B:2118 , PRO C:229 , ASP C:233 , HOH C:2204 , HOH C:2234BINDING SITE FOR RESIDUE EDO B1127
10BC1SOFTWAREHOH B:2069 , GLY C:46 , HIS C:323 , LEU C:325 , PHE C:335 , HOH C:2194BINDING SITE FOR RESIDUE EDO C1578
11BC2SOFTWARESER B:71 , THR B:73 , ASN C:43 , LYS C:48 , HOH C:2010 , HOH C:2015BINDING SITE FOR RESIDUE EDO C1579
12BC3SOFTWAREGLY A:50 , LYS A:51 , THR A:52 , PHE A:86 , ASP A:88 , HOH A:2082 , VAL C:309 , ASN C:310 , LYS C:559BINDING SITE FOR RESIDUE EDO A1102
13BC4SOFTWAREASP C:286 , ALA C:289 , ILE C:539 , HOH C:2225BINDING SITE FOR RESIDUE EDO C1580
14BC5SOFTWARETYR A:32 , MET A:76 , ASP A:78 , ASP A:79BINDING SITE FOR RESIDUE EDO A1103
15BC6SOFTWAREGLY A:27 , LYS A:29 , ASP A:67 , ASP A:68 , HOH A:2032 , HOH A:2038BINDING SITE FOR RESIDUE EDO A1104
16BC7SOFTWAREPHE A:42 , GLU A:59 , MET B:83 , GLU B:84 , HOH B:2098 , HOH B:2143BINDING SITE FOR RESIDUE EDO B1128
17BC8SOFTWARETYR C:35 , TYR C:83 , ILE C:97 , GLU C:429 , HOH C:2037 , HOH C:2048 , HOH C:2412BINDING SITE FOR RESIDUE EDO C1581
18BC9SOFTWARELYS C:33 , TYR C:35 , HOH C:2048BINDING SITE FOR RESIDUE EDO C1582
19CC1SOFTWAREHIS C:222 , GLU C:223 , HIS C:249 , GLY C:280 , HIS C:323 , ARG C:339 , HOH C:2196 , HOH C:2199 , HOH C:2243BINDING SITE FOR RESIDUE SO4 C1583
20CC2SOFTWAREHIS C:137 , KCX C:220 , HIS C:275 , ASP C:363 , NI C:600 , NI C:601 , HOH C:2143 , HOH C:2165 , HOH C:2243BINDING SITE FOR RESIDUE OH C1584
21CC3SOFTWARESER C:204 , ILE C:205 , EDO C:1573 , HOH C:2180 , HOH C:2184BINDING SITE FOR RESIDUE SO4 C1585
22CC4SOFTWAREMET A:70 , GLU A:71 , ARG C:566BINDING SITE FOR RESIDUE SO4 A1105
23CC5SOFTWAREARG B:116 , HOH B:2135BINDING SITE FOR RESIDUE SO4 B1129
24CC6SOFTWAREVAL C:558 , LYS C:559 , GLU C:560 , HOH C:2397BINDING SITE FOR RESIDUE SO4 C1586
25CC7SOFTWARETHR B:29 , ILE B:30 , ARG B:31 , HOH B:2052 , HOH B:2053 , HOH B:2081BINDING SITE FOR RESIDUE SO4 B1130
26CC8SOFTWARELYS C:169 , VAL C:321 , CYS C:322 , PRO C:469 , THR C:470 , HOH C:2162 , HOH C:2414BINDING SITE FOR RESIDUE DBX C1587
27CC9SOFTWAREGLN C:387 , ARG C:388 , THR C:554 , CYS C:555 , GLU C:556 , HOH C:2415 , HOH C:2416BINDING SITE FOR RESIDUE DBX C1588

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FSD)

(-) 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 5FSD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FSD)

(-) Exons   (0, 0)

(no "Exon" information available for 5FSD)

(-) 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 ---------------------------------------------------------------------------------------------------- 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
                 5fsd A   1 mHLNPAEKEKLQIFLASELALKRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS 100
                            |       10        20        30        40        50        60        70        80        90       100
                            |                                                                                                   
                            1-CXM                                                                                               


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               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
                 5fsd 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fsd C   1 MKINRQQYAESYGPTVGDQVRLADTDLWIEVEKDYTTYGDEANFGGGKVLREGMGENGTYTRTENVLDLLLTNALILDYTGIYKADIGVKDGYIVGIGKGGNPDIMDGVTPNMIVGTATEVIAAEGKIVTAGGIDTHVHFINPDQVDVALANGITTLFGGGTGPAEGSKATTVTPGPWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGAAGLkIHEDWGATPASIDRSLTVADEADVQVAIHSDTLNEAGFLEDTLRAINGRVIHSFHVEGAGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIRPETIAAEDILHDLGIISMMSTDALAMGRAGEMVLRTWQTADKMKKQRGPLAEEKNGSDNFRAKRYVSKYTINPAIAQGIAHEVGSIEEGKFADLVLWEPKFFGVKADRVIKGGIIAYAQIGDPSASIPTPQPVMGRRMYGTVGDLIHDTNITFMSKSSIQQGVPAKLGLKRRIGTVKNCRNIGKKDMKWNDVTTDIDINPETYEVKVDGEVLTCEPVKELPMAQRYFLF 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
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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  (0, 0)

(no "SCOP Domain" information available for 5FSD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FSD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FSD)

(-) Gene Ontology  (9, 19)

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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 4ubp 5a6t 5fse
        URE2_SPOPA | P41021: 1ie7 1s3t 1ubp 2ubp 3ubp 4ac7 4ceu 4cex 4ubp 5a6t 5fse 5g4h
        URE3_SPOPA | P41022: 1ie7 1s3t 1ubp 2ubp 3ubp 4ac7 4ceu 4cex 4ubp 5a6t 5fse 5g4h

(-) Related Entries Specified in the PDB File

5fse 2.07 A RESOLUTION 1,4-BENZOQUINONE INHIBITED SPOROSARCINA PASTEURII UREASE