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(-) Description

Title :  2.07 A RESOLUTION 1,4-BENZOQUINONE 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 :  2.07
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (3x)
Keywords :  Hydrolase, Urease, Sporosarcina Pasteurii, Nickel, Metalloenzyme, 1, 4-Benzoquinone (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 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
 
Molecule 3 - 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

 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, 26)

Asymmetric Unit (7, 26)
No.NameCountTypeFull Name
1CXM1Mod. Amino AcidN-CARBOXYMETHIONINE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3HQE2Ligand/IonBENZENE-1,4-DIOL
4KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
5NI2Ligand/IonNICKEL (II) ION
6OH1Ligand/IonHYDROXIDE ION
7SO49Ligand/IonSULFATE ION
Biological Unit 1 (5, 69)
No.NameCountTypeFull Name
1CXM3Mod. Amino AcidN-CARBOXYMETHIONINE
2EDO30Ligand/Ion1,2-ETHANEDIOL
3HQE6Ligand/IonBENZENE-1,4-DIOL
4KCX3Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
5NI-1Ligand/IonNICKEL (II) ION
6OH-1Ligand/IonHYDROXIDE ION
7SO427Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREKCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , NI C:601 , OH C:1580 , HOH C:2111BINDING SITE FOR RESIDUE NI C 600
02AC2SOFTWAREHIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , NI C:600 , OH C:1580 , HOH C:2094BINDING SITE FOR RESIDUE NI C 601
03AC3SOFTWAREGLY A:50 , LYS A:51 , THR A:52 , ASP A:88 , VAL C:309 , ASN C:310 , LYS C:559BINDING SITE FOR RESIDUE EDO A1101
04AC4SOFTWAREASP C:286 , ALA C:289 , ILE C:537 , ASP C:538 , ILE C:539BINDING SITE FOR RESIDUE EDO C1571
05AC5SOFTWAREVAL B:85 , GLU B:86BINDING SITE FOR RESIDUE EDO B1127
06AC6SOFTWARETHR C:37 , TYR C:38 , EDO C:1575 , HOH C:2293BINDING SITE FOR RESIDUE EDO C1572
07AC7SOFTWARETYR C:60 , ASN C:65 , ILE C:114 , SO4 C:1582 , HOH C:2081BINDING SITE FOR RESIDUE EDO C1573
08AC8SOFTWAREPRO C:143 , GLY C:189 , ARG C:478 , HOH C:2119BINDING SITE FOR RESIDUE EDO C1574
09AC9SOFTWAREASP C:34 , THR C:36 , TYR C:38 , EDO C:1572 , HOH C:2026BINDING SITE FOR RESIDUE EDO C1575
10BC1SOFTWAREILE C:500 , ARG C:513 , ILE C:514 , HOH C:2295BINDING SITE FOR RESIDUE EDO C1576
11BC2SOFTWAREASP C:34 , TYR C:35 , SO4 C:1581 , HOH C:2026BINDING SITE FOR RESIDUE EDO C1577
12BC3SOFTWARETYR C:93 , GLU C:423 , GLN C:501 , ARG C:513 , ILE C:514BINDING SITE FOR RESIDUE EDO C1578
13BC4SOFTWAREHIS C:222 , HIS C:249 , GLY C:280 , HIS C:323 , ARG C:339 , HOH C:2111 , HOH C:2134 , HOH C:2172BINDING SITE FOR RESIDUE SO4 C1579
14BC5SOFTWAREHIS C:137 , KCX C:220 , HIS C:275 , ASP C:363 , NI C:600 , NI C:601 , HOH C:2094 , HOH C:2111 , HOH C:2172BINDING SITE FOR RESIDUE OH C1580
15BC6SOFTWARELEU B:112 , ARG B:116BINDING SITE FOR RESIDUE SO4 B1128
16BC7SOFTWARELYS C:33 , TYR C:35 , EDO C:1577 , HOH C:2297BINDING SITE FOR RESIDUE SO4 C1581
17BC8SOFTWARESER C:204 , ILE C:205 , EDO C:1573 , HOH C:2123BINDING SITE FOR RESIDUE SO4 C1582
18BC9SOFTWAREGLN C:387 , ARG C:388 , THR C:554 , CYS C:555 , GLU C:556 , SO4 C:1588 , HOH C:2298BINDING SITE FOR RESIDUE HQE C1583
19CC1SOFTWAREGLN A:81 , VAL C:321 , CYS C:322 , ILE C:468 , PRO C:469 , THR C:470 , HOH C:2108 , HOH C:2110BINDING SITE FOR RESIDUE HQE C1584
20CC2SOFTWAREVAL C:558 , LYS C:559 , GLU C:560BINDING SITE FOR RESIDUE SO4 C1585
21CC3SOFTWAREMET A:70 , GLU A:71BINDING SITE FOR RESIDUE SO4 A1102
22CC4SOFTWAREASP C:107 , GLY C:108 , HOH C:2077BINDING SITE FOR RESIDUE SO4 C1586
23CC5SOFTWARESER B:71 , GLY B:72 , TYR C:12 , LYS C:48 , HOH C:2008 , HOH C:2299BINDING SITE FOR RESIDUE SO4 C1587
24CC6SOFTWAREARG C:388 , HQE C:1583 , HOH C:2300BINDING SITE FOR RESIDUE SO4 C1588

(-) SS Bonds  (0, 0)

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

(-) 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 5FSE)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FSE)

(-) 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
                 5fse 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
                 5fse 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....hhhhhhhhhhh...eeeee.hhh.hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhh...eee............hhhhhhhh..eee...........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh...............eeeehhhhh.....eeee..eeeeeee.............eeee.hhhhhhhhhhh.eeeeehhhhhhhhhhhhh...eeeee......hhhhh........eee......eee..eee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fse 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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  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 5FSE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4ubp 5a6t 5fsd
        URE2_SPOPA | P41021: 1ie7 1s3t 1ubp 2ubp 3ubp 4ac7 4ceu 4cex 4ubp 5a6t 5fsd 5g4h
        URE3_SPOPA | P41022: 1ie7 1s3t 1ubp 2ubp 3ubp 4ac7 4ceu 4cex 4ubp 5a6t 5fsd 5g4h

(-) Related Entries Specified in the PDB File

5fsd 1.75 A RESOLUTION 2,5-DIHYDROXYBENZENSULFONATE INHIBITED SPOROSARCINA PASTEURII UREASE