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(-) Description

Title :  CRYSTAL STRUCTURE OF KAIC-LIKE PROTEIN PH0186 FROM HYPERTHERMOPHILIC ARCHAEA PYROCOCCUS HORIKOSHII OT3
 
Authors :  H. Ming, K. Miyazono, M. Tanokura
Date :  08 Oct 08  (Deposition) - 24 Mar 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Kaic Like Protein, Atp-Binding, Nucleotide-Binding, Atp- Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -J. Kang, K. Kubota, H. Ming, K. Miyazono, M. Tanokura
Crystal Structure Of Kaic-Like Protein Ph0186 From Hyperthermophilic Archaea Pyrococcus Horikoshii Ot3
Proteins V. 75 1035 2009
PubMed-ID: 19274727  |  Reference-DOI: 10.1002/PROT.22367
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN PH0186
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Strain: OT3

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
3MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 30)
No.NameCountTypeFull Name
1ADP6Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:38 , GLY A:40 , THR A:41 , GLY A:42 , LYS A:43 , THR A:44 , THR A:45 , SER A:80 , PHE A:81 , ARG A:216 , ILE A:237 , MG A:1904 , HOH A:1912 , HOH A:1927 , HOH A:1928 , HOH A:1929 , LYS C:222 , MSE C:223 , GLU C:225 , THR C:226 , ARG C:227 , HIS C:228BINDING SITE FOR RESIDUE ADP A 1903
2AC2SOFTWARETHR A:44 , ADP A:1903 , HOH A:1905 , HOH A:1927 , HOH A:1928 , HOH A:1929BINDING SITE FOR RESIDUE MG A 1904
3AC3SOFTWARELYS A:222 , MSE A:223 , GLU A:225 , THR A:226 , ARG A:227 , HIS A:228 , GLY B:40 , THR B:41 , GLY B:42 , LYS B:43 , THR B:44 , THR B:45 , SER B:80 , PHE B:81 , ARG B:216 , ILE B:237 , MG B:1904 , HOH B:1918 , HOH B:1938 , HOH B:1939 , HOH B:1940BINDING SITE FOR RESIDUE ADP B 1903
4AC4SOFTWARETHR B:44 , ADP B:1903 , HOH B:1909 , HOH B:1938 , HOH B:1939 , HOH B:1940BINDING SITE FOR RESIDUE MG B 1904
5AC5SOFTWARELYS B:222 , MSE B:223 , GLU B:225 , THR B:226 , ARG B:227 , HIS B:228 , GLY C:40 , THR C:41 , GLY C:42 , LYS C:43 , THR C:44 , THR C:45 , SER C:80 , PHE C:81 , ARG C:216 , ILE C:237 , MG C:1904 , HOH C:1919 , HOH C:1923 , HOH C:1928 , HOH C:1930 , HOH C:1931BINDING SITE FOR RESIDUE ADP C 1903
6AC6SOFTWARETHR C:44 , ADP C:1903 , HOH C:1928 , HOH C:1929 , HOH C:1930 , HOH C:1931BINDING SITE FOR RESIDUE MG C 1904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZTS)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asp A:142 -Ser A:143
2Lys A:210 -Asn A:211
3Asp B:142 -Ser B:143
4Asp C:142 -Ser C:143
5Lys C:210 -Asn C:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZTS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZTS)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZTS)

(-) 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:216
 aligned with O57925_PYRHO | O57925 from UniProtKB/TrEMBL  Length:251

    Alignment length:239
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
         O57925_PYRHO     8 PVRRVKSGIPGFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEERARDLRREMASFGWDFEKYEKEGKIAIVDGVSSVVGLPSEEKFVLEDRFNVDNFLRYIYRVVKAINAKRLVIDSIPSIALRLEEERKIREVLLKLNTILLEMGVTTILTTEAPDPQHGKLSRYGIEEFIARGVIVLDLQEKNIELKRYVLIRKMRETRHSMKKYPFEIGPNGIVVYP 246
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......hhhhh...ee...eeeee.....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...hhhhhhhh..eeee.-------------------.hhhhhhhhhhhhhhhh...eeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeee...----.......hhhhhh.eeeeeeeee....eeeeeeeeee........eeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zts A   8 PVRRVKSGIPGFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEERARDLRREmASFGWDFEKYEKEGKIAIVD-------------------FNVDNFLRYIYRVVKAINAKRLVIDSIPSIALRLEEERKIREVLLKLNTILLEmGVTTILTTEAP----GKLSRYGIEEFIARGVIVLDLQEKNIELKRYVLIRKmRETRHSmKKYPFEIGPNGIVVYP 246
                                    17        27        37        47        57        67        77|       87        97|        -         -|      127       137       147       157       167   |   177    |  187       197       207       217     | 227  |    237         
                                                                                                 78-MSE              98                 118                                                  171-MSE    182  187                                 223-MSE  |                
                                                                                                                                                                                                                                                        230-MSE            


Chain B from PDB  Type:PROTEIN  Length:216
 aligned with O57925_PYRHO | O57925 from UniProtKB/TrEMBL  Length:251

    Alignment length:239
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
         O57925_PYRHO     8 PVRRVKSGIPGFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEERARDLRREMASFGWDFEKYEKEGKIAIVDGVSSVVGLPSEEKFVLEDRFNVDNFLRYIYRVVKAINAKRLVIDSIPSIALRLEEERKIREVLLKLNTILLEMGVTTILTTEAPDPQHGKLSRYGIEEFIARGVIVLDLQEKNIELKRYVLIRKMRETRHSMKKYPFEIGPNGIVVYP 246
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......hhhhhh..ee...eeeee.....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...hhhhhhhh..eeee.-------------------.hhhhhhhhhhhhhhhh...eeeeehhhhhhh...hhhhhhhhhhhhhhhhhhhh.eeeeee...----.......hhhhhh.eeeeeeeeee..eeeeeeeeeee.........eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zts B   8 PVRRVKSGIPGFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEERARDLRREmASFGWDFEKYEKEGKIAIVD-------------------FNVDNFLRYIYRVVKAINAKRLVIDSIPSIALRLEEERKIREVLLKLNTILLEmGVTTILTTEAP----GKLSRYGIEEFIARGVIVLDLQEKNIELKRYVLIRKmRETRHSmKKYPFEIGPNGIVVYP 246
                                    17        27        37        47        57        67        77|       87        97|        -         -|      127       137       147       157       167   |   177    |  187       197       207       217     | 227  |    237         
                                                                                                 78-MSE              98                 118                                                  171-MSE    182  187                                 223-MSE  |                
                                                                                                                                                                                                                                                        230-MSE            


Chain C from PDB  Type:PROTEIN  Length:226
 aligned with O57925_PYRHO | O57925 from UniProtKB/TrEMBL  Length:251

    Alignment length:239
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
         O57925_PYRHO     8 PVRRVKSGIPGFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEERARDLRREMASFGWDFEKYEKEGKIAIVDGVSSVVGLPSEEKFVLEDRFNVDNFLRYIYRVVKAINAKRLVIDSIPSIALRLEEERKIREVLLKLNTILLEMGVTTILTTEAPDPQHGKLSRYGIEEFIARGVIVLDLQEKNIELKRYVLIRKMRETRHSMKKYPFEIGPNGIVVYP 246
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----KaiC-2ztsC01 C:12-246                                                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) ----KaiC-2ztsC02 C:12-246                                                                                                                                                                                                                       Pfam domains (2)
           Pfam domains (3) ----KaiC-2ztsC03 C:12-246                                                                                                                                                                                                                       Pfam domains (3)
         Sec.struct. author ...ee......hhhhh...ee...eeeee.....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...hhhhhhhh..eeee...........---------.hhhhhhhhhhhhhhhhh..eeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eeeeee...----.......hhhhhh.eeeeeeeee....eeeeeeeeee.........eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zts C   8 PVRRVKSGIPGFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEERARDLRREmASFGWDFEKYEKEGKIAIVDGVSSVVGLPS---------FNVDNFLRYIYRVVKAINAKRLVIDSIPSIALRLEEERKIREVLLKLNTILLEmGVTTILTTEAP----GKLSRYGIEEFIARGVIVLDLQEKNIELKRYVLIRKmRETRHSmKKYPFEIGPNGIVVYP 246
                                    17        27        37        47        57        67        77|       87        97       107|        -|      127       137       147       157       167   |   177    |  187       197       207       217     | 227  |    237         
                                                                                                 78-MSE                       108       118                                                  171-MSE    182  187                                 223-MSE  |                
                                                                                                                                                                                                                                                        230-MSE
   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 2ZTS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZTS)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (O57925_PYRHO | O57925)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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