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(-) Description

Title :  1.50 A RESOLUTION CATECHOL (1,2-DIHYDROXYBENZENE) INHIBITED SPOROSARCINA PASTEURII UREASE
 
Authors :  L. Mazzei, M. Cianci, F. Musiani, S. Ciurli
Date :  13 May 16  (Deposition) - 07 Dec 16  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (3x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Mazzei, M. Cianci, F. Musiani, G. Lente, M. Palombo, S. Ciurli
Inactivation Of Urease By Catechol: Kinetics And Structure.
J. Inorg. Biochem. V. 166 182 2016
PubMed-ID: 27888701  |  Reference-DOI: 10.1016/J.JINORGBIO.2016.11.016

(-) 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)
    Strain: DSM 33
    Synonym: UREA AMIDOHYDROLASE SUBUNIT GAMMA
 
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)
    Strain: DSM 33
    Synonym: UREA AMIDOHYDROLASE SUBUNIT BETA
 
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)
    Strain: DSM 33
    Synonym: UREA AMIDOHYDROLASE SUBUNIT ALPHA

 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, 27)

Asymmetric Unit (7, 27)
No.NameCountTypeFull Name
1CAQ1Ligand/IonCATECHOL
2CXM1Mod. Amino AcidN-CARBOXYMETHIONINE
3EDO15Ligand/Ion1,2-ETHANEDIOL
4KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
5NI2Ligand/IonNICKEL (II) ION
6OH1Ligand/IonHYDROXIDE ION
7SO46Ligand/IonSULFATE ION
Biological Unit 1 (5, 72)
No.NameCountTypeFull Name
1CAQ3Ligand/IonCATECHOL
2CXM3Mod. Amino AcidN-CARBOXYMETHIONINE
3EDO45Ligand/Ion1,2-ETHANEDIOL
4KCX3Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
5NI-1Ligand/IonNICKEL (II) ION
6OH-1Ligand/IonHYDROXIDE ION
7SO418Ligand/IonSULFATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREKCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , NI C:601 , OH C:1573 , HOH C:2176BINDING SITE FOR RESIDUE NI C 600
02AC2SOFTWAREHIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , NI C:600 , OH C:1573 , HOH C:2153BINDING SITE FOR RESIDUE NI C 601
03AC3SOFTWAREHIS C:222 , GLU C:223 , ASP C:224 , HIS C:249 , GLY C:280 , HIS C:323 , ARG C:339 , HOH C:2176 , HOH C:2206 , HOH C:2208 , HOH C:2248 , HOH C:2288BINDING SITE FOR RESIDUE SO4 C1572
04AC4SOFTWAREHIS C:137 , KCX C:220 , HIS C:275 , ASP C:363 , NI C:600 , NI C:601 , HOH C:2153 , HOH C:2176 , HOH C:2248BINDING SITE FOR RESIDUE OH C1573
05AC5SOFTWAREVAL C:558 , LYS C:559 , GLU C:560 , HOH C:2415BINDING SITE FOR RESIDUE SO4 C1574
06AC6SOFTWAREMET A:70 , GLU A:71 , HOH A:2095 , ARG C:566BINDING SITE FOR RESIDUE SO4 A1101
07AC7SOFTWAREARG B:116BINDING SITE FOR RESIDUE SO4 B1127
08AC8SOFTWAREGLY A:50 , LYS A:51 , THR A:52 , PHE A:86 , ASP A:88 , VAL C:309 , ASN C:310 , LYS C:559 , HOH C:2425BINDING SITE FOR RESIDUE EDO C1575
09AC9SOFTWAREASP C:34 , THR C:36 , TYR C:38 , HOH C:2048 , HOH C:2060 , HOH C:2426BINDING SITE FOR RESIDUE EDO C1576
10BC1SOFTWAREASP C:286 , ALA C:289 , ILE C:537 , ILE C:539 , HOH C:2232 , HOH C:2404BINDING SITE FOR RESIDUE EDO C1577
11BC2SOFTWAREGLY A:27 , LEU A:28 , LYS A:29 , ASP A:67 , ASP A:68 , HOH A:2032 , HOH A:2040BINDING SITE FOR RESIDUE EDO A1102
12BC3SOFTWAREHOH B:2079 , GLY C:46 , HIS C:323 , LEU C:325 , PHE C:335 , HOH C:2067 , HOH C:2203BINDING SITE FOR RESIDUE EDO C1578
13BC4SOFTWARESER B:71 , TYR C:12 , LYS C:48 , HOH C:2019BINDING SITE FOR RESIDUE EDO C1579
14BC5SOFTWARETYR C:35 , TYR C:83 , ILE C:97 , GLU C:429 , HOH C:2045 , HOH C:2428BINDING SITE FOR RESIDUE EDO C1580
15BC6SOFTWAREASN A:4 , LYS A:10 , HOH A:2088 , PHE C:568 , PHE C:570 , HOH C:2291 , HOH C:2429BINDING SITE FOR RESIDUE EDO C1581
16BC7SOFTWAREASP B:101 , HOH B:2127 , PRO C:229 , ASP C:233 , HOH C:2213 , HOH C:2240BINDING SITE FOR RESIDUE EDO B1128
17BC8SOFTWARETHR C:237 , ASP C:240 , ARG C:269BINDING SITE FOR RESIDUE EDO C1582
18BC9SOFTWAREHIS C:422 , GLU C:423 , GLY C:430 , GLN C:501 , HOH C:2327 , HOH C:2383BINDING SITE FOR RESIDUE EDO C1583
19CC1SOFTWARETYR C:93 , GLU C:423 , GLN C:501 , ARG C:513 , ILE C:514 , HOH C:2431BINDING SITE FOR RESIDUE EDO C1584
20CC2SOFTWARECXM A:1 , TYR A:32 , ASP A:79 , HOH A:2085 , HOH A:2096BINDING SITE FOR RESIDUE EDO A1103
21CC3SOFTWAREPRO C:143 , GLY C:189 , PRO C:191 , ARG C:478 , HOH C:2071 , HOH C:2158BINDING SITE FOR RESIDUE EDO C1585
22CC4SOFTWAREPRO C:177 , TRP C:178 , GLU C:181BINDING SITE FOR RESIDUE EDO C1586
23CC5SOFTWAREILE B:30 , ARG B:31 , HOH B:2058BINDING SITE FOR RESIDUE SO4 B1129
24CC6SOFTWARESER C:204 , ILE C:205 , HOH C:2190 , HOH C:2194BINDING SITE FOR RESIDUE SO4 C1587
25CC7SOFTWAREHIS C:137 , KCX C:220 , HIS C:275 , ASP C:363 , NI C:600 , NI C:601 , HOH C:2153 , HOH C:2176 , HOH C:2248BINDING SITE FOR RESIDUE OH C1573
26CC8SOFTWAREMET C:318 , LEU C:319 , MET C:320 , VAL C:321 , HIS C:323 , HIS C:324 , ILE C:468 , PRO C:469 , THR C:470 , HOH C:2172 , HOH C:2173 , HOH C:2424BINDING SITE FOR DI-PEPTIDE CYS C 322 AND CAQ C1571

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G4H)

(-) 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 5G4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G4H)

(-) Exons   (0, 0)

(no "Exon" information available for 5G4H)

(-) 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
                 5g4h 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
                 5g4h 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.........hhhhhhhhhhhhhhhhhhhhh...............eeeehhhhh.....eeee..eeeeeee.............eeee.hhhhhhhhhhh.eeeehhhhhhhhhhhhhh...eeee.......hhhhh........eee......eee..ee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5g4h 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 5G4H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G4H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G4H)

(-) Gene Ontology  (6, 10)

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  5g4h
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 Related Entries

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

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

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