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(-) Description

Title :  1.65 A RESOLUTION SULPHITE INHIBITED SPOROSARCINA PASTEURII UREASE
 
Authors :  L. Mazzei, M. Cianci, S. Benini, L. Bertini, F. Musiani, S. Ciurli
Date :  01 Jul 15  (Deposition) - 02 Dec 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (3x)
Keywords :  Hydrolase, Urease, Nickel, Metalloenzyme, Sulfite (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Mazzei, M. Cianci, S. Benini, L. Bertini, F. Musiani, S. Ciurli
Kinetic And Structural Studies Reveal A Unique Binding Mode Of Sulfite To The Nickel Center In Urease.
J. Inorg. Biochem. V. 154 42 2015
PubMed-ID: 26580226  |  Reference-DOI: 10.1016/J.JINORGBIO.2015.11.003

(-) 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
 
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
 
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

 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, 13)

Asymmetric Unit (6, 13)
No.NameCountTypeFull Name
1CXM1Mod. Amino AcidN-CARBOXYMETHIONINE
2EDO7Ligand/Ion1,2-ETHANEDIOL
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4NI2Ligand/IonNICKEL (II) ION
5SO31Ligand/IonSULFITE ION
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 33)
No.NameCountTypeFull Name
1CXM3Mod. Amino AcidN-CARBOXYMETHIONINE
2EDO21Ligand/Ion1,2-ETHANEDIOL
3KCX3Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4NI-1Ligand/IonNICKEL (II) ION
5SO33Ligand/IonSULFITE ION
6SO43Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREKCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , NI C:1572 , SO3 C:1573BINDING SITE FOR RESIDUE NI C1571
02AC2SOFTWAREHIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , NI C:1571 , SO3 C:1573BINDING SITE FOR RESIDUE NI C1572
03AC3SOFTWAREHIS C:137 , HIS C:139 , ALA C:170 , KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , ASP C:363 , ALA C:366 , NI C:1571 , NI C:1572BINDING SITE FOR RESIDUE SO3 C1573
04AC4SOFTWAREASP C:34 , THR C:36 , TYR C:38 , HOH C:2038 , HOH C:2050BINDING SITE FOR RESIDUE EDO C1574
05AC5SOFTWAREGLY A:50 , LYS A:51 , THR A:52 , PHE A:86 , ASP A:88 , HOH A:2096 , VAL C:309 , ASN C:310 , LYS C:559BINDING SITE FOR RESIDUE EDO A1101
06AC6SOFTWAREASP C:286 , ALA C:289 , ILE C:537 , ILE C:539 , HOH C:2224BINDING SITE FOR RESIDUE EDO C1575
07AC7SOFTWARETYR C:35 , TYR C:83 , ILE C:97 , GLU C:429 , HOH C:2035 , HOH C:2399BINDING SITE FOR RESIDUE EDO C1576
08AC8SOFTWAREASP B:101 , HOH B:2119 , PRO C:229 , ASP C:233 , HOH C:2203 , HOH C:2231BINDING SITE FOR RESIDUE EDO C1577
09AC9SOFTWAREHOH B:2070 , GLY C:46 , LEU C:325 , HOH C:2193 , HOH C:2264BINDING SITE FOR RESIDUE EDO B1127
10BC1SOFTWAREASN A:4 , ALA A:6 , LYS A:10 , HOH A:2089 , HOH A:2097 , PHE C:568 , PHE C:570 , HOH C:2279BINDING SITE FOR RESIDUE EDO A1102
11BC2SOFTWAREARG B:116 , HOH B:2133BINDING SITE FOR RESIDUE SO4 B1128

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A6T)

(-) 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 5A6T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A6T)

(-) Exons   (0, 0)

(no "Exon" information available for 5A6T)

(-) 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
                 5a6t 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
                 5a6t 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.........ee......eee..ee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a6t 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
   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  (0, 0)

(no "SCOP Domain" information available for 5A6T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A6T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A6T)

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

(-) Related Entries Specified in the PDB File

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