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(-) Description

Title :  D-HYDANTOINASE (DIHYDROPYRIMIDINASE) FROM THERMUS SP. IN SPACE GROUP C2221
 
Authors :  J. Abendroth, K. Niefind, D. Schomburg
Date :  20 Aug 01  (Deposition) - 27 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.29
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D,E,F  (1x)
Keywords :  Hydrolase, Hydantoinase, Dihydropyrimidinase, Cyclic Amidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abendroth, K. Niefind, D. Schomburg
X-Ray Structure Of A Dihydropyrimidinase From Thermus Sp. At 1. 3 A Resolution
J. Mol. Biol. V. 320 143 2002
PubMed-ID: 12079340  |  Reference-DOI: 10.1016/S0022-2836(02)00422-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDANTOINASE
    Chains: A, B, C, D, E, F
    EC Number: 3.5.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: THERMUS SP.
    Organism Taxid: 275
    Other Details: KCX IS A NZ-CARBOXYLATED LYSINE
    Synonym: DIHYDROPYRIMIDINASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): AB    
Biological Unit 2 (1x):   CDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 29)

Asymmetric Unit (4, 29)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2KCX6Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO49Ligand/IonSULFATE ION
4ZN12Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO47Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREKCX A:150 , HIS A:183 , HIS A:239 , ZN A:1461 , HOH A:2605 , HOH A:2606BINDING SITE FOR RESIDUE ZN A1460
02AC2SOFTWAREHIS A:59 , HIS A:61 , KCX A:150 , ASP A:315 , ZN A:1460 , HOH A:2606BINDING SITE FOR RESIDUE ZN A1461
03AC3SOFTWARELYS A:370 , LYS A:373 , HOH A:2507 , HOH A:2508 , HOH A:2607 , HOH A:2608 , HOH A:2609 , HIS B:361 , ARG B:362BINDING SITE FOR RESIDUE SO4 A1462
04AC4SOFTWAREKCX B:150 , HIS B:183 , HIS B:239 , ZN B:1461 , HOH B:2584 , HOH B:2585BINDING SITE FOR RESIDUE ZN B1460
05AC5SOFTWAREHIS B:59 , HIS B:61 , KCX B:150 , ASP B:315 , ZN B:1460 , HOH B:2585BINDING SITE FOR RESIDUE ZN B1461
06AC6SOFTWAREHIS A:361 , LYS B:370 , LYS B:373 , HOH B:2472 , HOH B:2473 , HOH B:2586 , HOH B:2587 , HOH B:2588BINDING SITE FOR RESIDUE SO4 B1462
07AC7SOFTWAREKCX C:150 , HIS C:183 , HIS C:239 , ZN C:1461 , HOH C:2654 , HOH C:2655BINDING SITE FOR RESIDUE ZN C1460
08AC8SOFTWAREHIS C:59 , HIS C:61 , KCX C:150 , ASP C:315 , ZN C:1460 , HOH C:2655BINDING SITE FOR RESIDUE ZN C1461
09AC9SOFTWARELYS C:370 , LYS C:373 , HOH C:2548 , HOH C:2549 , HOH C:2656 , HOH C:2657 , HOH C:2658 , HIS D:361 , ARG D:362BINDING SITE FOR RESIDUE SO4 C1462
10BC1SOFTWAREGLN C:107 , LYS C:110 , HOH C:2661 , HOH C:2662 , EPE F:1463BINDING SITE FOR RESIDUE SO4 C1463
11BC2SOFTWAREKCX D:150 , HIS D:183 , HIS D:239 , ZN D:1461 , HOH D:2555 , HOH D:2556BINDING SITE FOR RESIDUE ZN D1460
12BC3SOFTWAREHIS D:59 , HIS D:61 , KCX D:150 , ASP D:315 , ZN D:1460 , HOH D:2556BINDING SITE FOR RESIDUE ZN D1461
13BC4SOFTWAREHIS C:361 , LYS D:370 , LYS D:373 , HOH D:2456 , HOH D:2457 , HOH D:2557 , HOH D:2558 , HOH D:2559 , HOH D:2560BINDING SITE FOR RESIDUE SO4 D1462
14BC5SOFTWAREKCX E:150 , HIS E:183 , HIS E:239 , ZN E:1461 , HOH E:2680 , HOH E:2681BINDING SITE FOR RESIDUE ZN E1460
15BC6SOFTWAREHIS E:59 , HIS E:61 , KCX E:150 , ASP E:315 , ZN E:1460 , HOH E:2681BINDING SITE FOR RESIDUE ZN E1461
16BC7SOFTWARELYS E:370 , LYS E:373 , HOH E:2555 , HOH E:2556 , HOH E:2682 , HOH E:2683 , HOH E:2685 , HOH E:2687 , HIS F:361BINDING SITE FOR RESIDUE SO4 E1462
17BC8SOFTWAREEPE D:1463 , GLN E:107 , LYS E:110 , HOH E:2688 , HOH E:2689BINDING SITE FOR RESIDUE SO4 E1463
18BC9SOFTWAREARG E:438 , HOH E:2690 , HOH E:2691BINDING SITE FOR RESIDUE SO4 E1464
19CC1SOFTWAREKCX F:150 , HIS F:183 , HIS F:239 , ZN F:1461 , HOH F:2591 , HOH F:2592BINDING SITE FOR RESIDUE ZN F1460
20CC2SOFTWAREHIS F:59 , HIS F:61 , KCX F:150 , ASP F:315 , ZN F:1460 , HOH F:2592BINDING SITE FOR RESIDUE ZN F1461
21CC3SOFTWAREHIS E:361 , HOH E:2553 , LYS F:370 , LYS F:373 , HOH F:2483 , HOH F:2485 , HOH F:2594 , HOH F:2595 , HOH F:2596BINDING SITE FOR RESIDUE SO4 F1462
22CC4SOFTWAREVAL D:428 , ASP D:439 , HOH D:2524 , HOH D:2562 , HOH D:2563 , HOH D:2564 , GLN E:107 , GLU E:140 , SO4 E:1463BINDING SITE FOR RESIDUE EPE D1463
23CC5SOFTWARELEU C:103 , GLN C:107 , GLU C:140 , SO4 C:1463 , SER F:427 , VAL F:428 , ASP F:439 , HOH F:2597 , HOH F:2598 , HOH F:2599 , HOH F:2600BINDING SITE FOR RESIDUE EPE F1463

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GKP)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:288 -Pro A:289
2Phe A:378 -Pro A:379
3Ser B:288 -Pro B:289
4Phe B:378 -Pro B:379
5Ser C:288 -Pro C:289
6Phe C:378 -Pro C:379
7Ser D:288 -Pro D:289
8Phe D:378 -Pro D:379
9Ser E:288 -Pro E:289
10Phe E:378 -Pro E:379
11Ser F:288 -Pro F:289
12Phe F:378 -Pro F:379

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GKP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GKP)

(-) Exons   (0, 0)

(no "Exon" information available for 1GKP)

(-) 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:458
 aligned with Q7SIE9_THESP | Q7SIE9 from UniProtKB/TrEMBL  Length:458

    Alignment length:458
                                    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        
         Q7SIE9_THESP     1 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFKIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 458
               SCOP domains d1gkpa1 A:2-54,A:390-459 D-hydantoinase              d1gkpa2 A:55-389 D-hydantoinase                                                                                                                                                                                                                                                                                                                d1gkpa1 A:2-54,A:390-459 D-hydantoinase                                SCOP domains
               CATH domains 1gkpA01 A:2-53,A:389-396,A:424-444                  1gkpA02 A:54-383,A:399-423 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                     -----1gkpA01 --1gkpA02                  1gkpA01              --------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee..eeee.eeee......eee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....eee......hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeee....ee.hhhhh............ee..eeeeeee..eeeee..ee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gkp A   2 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFkIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 459
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451        
                                                                                                                                                                              150-KCX                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:458
 aligned with Q7SIE9_THESP | Q7SIE9 from UniProtKB/TrEMBL  Length:458

    Alignment length:458
                                    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        
         Q7SIE9_THESP     1 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFKIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 458
               SCOP domains d1gkpb1 B:2-54,B:390-459 D-hydantoinase              d1gkpb2 B:55-389 D-hydantoinase                                                                                                                                                                                                                                                                                                                d1gkpb1 B:2-54,B:390-459 D-hydantoinase                                SCOP domains
               CATH domains 1gkpB01 B:2-53,B:383-459 Urease, subunit C, domain 11gkpB02 B:54-382 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                              1gkpB01 B:2-53,B:383-459 Urease, subunit C, domain 1                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeeeee......eee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....eee......hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeee....ee.hhhhh............ee..eeeeeee..eeeee..ee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gkp B   2 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFkIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 459
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451        
                                                                                                                                                                              150-KCX                                                                                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:458
 aligned with Q7SIE9_THESP | Q7SIE9 from UniProtKB/TrEMBL  Length:458

    Alignment length:458
                                    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        
         Q7SIE9_THESP     1 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFKIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 458
               SCOP domains d1gkpc1 C:2-54,C:390-459 D-hydantoinase              d1gkpc2 C:55-389 D-hydantoinase                                                                                                                                                                                                                                                                                                                d1gkpc1 C:2-54,C:390-459 D-hydantoinase                                SCOP domains
               CATH domains 1gkpC01 C:2-53,C:389-396,C:424-444                  1gkpC02 C:54-383,C:399-423 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                     -----1gkpC01 --1gkpC02                  1gkpC01              --------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee..eeee.eeee......eee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....eee......hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeee....ee..................ee..eeeeeee..eeeee..ee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gkp C   2 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFkIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 459
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451        
                                                                                                                                                                              150-KCX                                                                                                                                                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:458
 aligned with Q7SIE9_THESP | Q7SIE9 from UniProtKB/TrEMBL  Length:458

    Alignment length:458
                                    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        
         Q7SIE9_THESP     1 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFKIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 458
               SCOP domains d1gkpd1 D:2-54,D:390-459 D-hydantoinase              d1gkpd2 D:55-389 D-hydantoinase                                                                                                                                                                                                                                                                                                                d1gkpd1 D:2-54,D:390-459 D-hydantoinase                                SCOP domains
               CATH domains 1gkpD01 D:2-53,D:389-396,D:424-444                  1gkpD02 D:54-383,D:399-423 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                     -----1gkpD01 --1gkpD02                  1gkpD01              --------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeeeee......eee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....eee......hhhhhhhhh.hhhhh........hhhhhhhhhh......hhhhhhhhhhhhhhhhh................eeeee....ee.hhhhh............ee..eeeeeee..eeeee..ee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gkp D   2 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFkIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 459
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451        
                                                                                                                                                                              150-KCX                                                                                                                                                                                                                                                                                                                 


Chain E from PDB  Type:PROTEIN  Length:458
 aligned with Q7SIE9_THESP | Q7SIE9 from UniProtKB/TrEMBL  Length:458

    Alignment length:458
                                    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        
         Q7SIE9_THESP     1 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFKIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 458
               SCOP domains d1gkpe1 E:2-54,E:390-459 D-hydantoinase              d1gkpe2 E:55-389 D-hydantoinase                                                                                                                                                                                                                                                                                                                d1gkpe1 E:2-54,E:390-459 D-hydantoinase                                SCOP domains
               CATH domains 1gkpE01 E:2-53,E:389-396,E:424-444                  1gkpE02 E:54-383,E:399-423 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                     -----1gkpE01 --1gkpE02                  1gkpE01              --------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeeeee......eee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....eee......hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeee....ee.hhhhh............ee..eeeeeee..eeeee..ee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gkp E   2 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFkIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 459
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451        
                                                                                                                                                                              150-KCX                                                                                                                                                                                                                                                                                                                 


Chain F from PDB  Type:PROTEIN  Length:458
 aligned with Q7SIE9_THESP | Q7SIE9 from UniProtKB/TrEMBL  Length:458

    Alignment length:458
                                    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        
         Q7SIE9_THESP     1 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFKIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 458
               SCOP domains d1gkpf1 F:2-54,F:390-459 D-hydantoinase              d1gkpf2 F:55-389 D-hydantoinase                                                                                                                                                                                                                                                                                                                d1gkpf1 F:2-54,F:390-459 D-hydantoinase                                SCOP domains
               CATH domains 1gkpF01 F:2-53,F:389-396,F:424-444                  1gkpF02 F:54-383,F:399-423 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                     -----1gkpF01 --1gkpF02                  1gkpF01              --------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee..eeee.eeee......eee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh....eee......hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeee....ee.hhhhh............ee..eeeeeee..eeeee..ee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gkp F   2 PLLIKNGEIITADSRYKADIYAEGETITRIGQNLEAPPGTEVIDATGKYVFPGFIDPHVHIYLPFMATFAKDTHETGSKAALMGGTTTYIEMCCPSRNDDALEGYQLWKSKAEGNSYCDYTFHMAVSKFDEKTEGQLREIVADGISSFkIFLSYKNFFGVDDGEMYQTLRLAKELGVIVTAHCENAELVGRLQQKLLSEGKTGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVHLSCKPALDAAMAAKARGVPIYIESVIPHFLLDKTYAERGGVEAMKYIMSPPLRDKRNQKVLWDALAQGFIDTVGTDHCPFDTEQKLLGKEAFTAIPNGIPAIEDRVNLLYTYGVSRGRLDIHRFVDAASTKAAKLFGLFPRKGTIAVGSDADLVVYDPQYRGTISVKTQHVNNDYNGFEGFEIDGRPSVVTVRGKVAVRDGQFVGEKGWGKLLRREPMYF 459
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451        
                                                                                                                                                                              150-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  (2, 12)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: Alpha-Beta Barrel (2994)
(-)
Topology: TIM Barrel (2806)
(-)
Homologous Superfamily: Metal-dependent hydrolases (190)
(-)
Thermus sp.. Organism_taxid: 275. (2)
1a1gkpB02B:54-382
1b1gkpA02A:54-383,A:399-423
1c1gkpC02C:54-383,C:399-423
1d1gkpD02D:54-383,D:399-423
1e1gkpE02E:54-383,E:399-423
1f1gkpF02F:54-383,F:399-423
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Roll (1513)
(-)
Topology: Urease, subunit C; domain 1 (95)
(-)
Homologous Superfamily: Urease, subunit C, domain 1 (95)
(-)
Thermus sp.. Organism_taxid: 275. (2)
2a1gkpB01B:2-53,B:383-459
2b1gkpA01A:2-53,A:389-396,A:424-444
2c1gkpC01C:2-53,C:389-396,C:424-444
2d1gkpD01D:2-53,D:389-396,D:424-444
2e1gkpE01E:2-53,E:389-396,E:424-444
2f1gkpF01F:2-53,F:389-396,F:424-444

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GKP)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q7SIE9_THESP | Q7SIE9)
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.
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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 Related Entries

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

UniProtKB/TrEMBL
        Q7SIE9_THESP | Q7SIE9: 1gkq

(-) Related Entries Specified in the PDB File

1gkq D-HYDANTOINASE (DIHYDROPYRIMIDINASE) FROM THERMUS SP. IN SPACE GROUP P212121