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(-) Description

Title :  CRYSTAL STRUCTURE OF POLYPHOSPHATE KINASE 2 FROM ARTHROBACTER AURESCENS TC1
 
Authors :  B. Nocek, C. Hatzos-Skintges, B. Feldmann, G. Babnigg, A. Joachimiak, Center For Structural Genomics (Mcsg)
Date :  11 Apr 11  (Deposition) - 01 Jun 11  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  A,B,C,D  (1x)
Biol. Unit 3:  B,D  (1x)
Keywords :  Psi-Biology, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, 3-Layer Alpha/Beta/Alpha Sandwich With The Central 5- Stranded, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, C. Hatzos-Skintges, B. Feldmann, G. Babnigg, A. Joachimiak
Crystal Structure Of Polyphosphate Kinase 2 From Arthrobacter Aurescens Tc1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE POLYPHOSPHATE KINASE 2 FAMILY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector: PMCSG19
    Gene: AAUR_2811
    Organism Scientific: ARTHROBACTER AURESCENS
    Organism Taxid: 290340
    Strain: TC1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x): ABCD
Biological Unit 3 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 43)

Asymmetric Unit (7, 43)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FLC4Ligand/IonCITRATE ANION
4MSE20Mod. Amino AcidSELENOMETHIONINE
5PG44Ligand/IonTETRAETHYLENE GLYCOL
6PGE4Ligand/IonTRIETHYLENE GLYCOL
7PO48Ligand/IonPHOSPHATE ION
Biological Unit 1 (6, 21)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FLC2Ligand/IonCITRATE ANION
4MSE10Mod. Amino AcidSELENOMETHIONINE
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE2Ligand/IonTRIETHYLENE GLYCOL
7PO45Ligand/IonPHOSPHATE ION
Biological Unit 2 (6, 42)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FLC4Ligand/IonCITRATE ANION
4MSE20Mod. Amino AcidSELENOMETHIONINE
5PG44Ligand/IonTETRAETHYLENE GLYCOL
6PGE4Ligand/IonTRIETHYLENE GLYCOL
7PO48Ligand/IonPHOSPHATE ION
Biological Unit 3 (6, 21)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FLC2Ligand/IonCITRATE ANION
4MSE10Mod. Amino AcidSELENOMETHIONINE
5PG43Ligand/IonTETRAETHYLENE GLYCOL
6PGE2Ligand/IonTRIETHYLENE GLYCOL
7PO43Ligand/IonPHOSPHATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:274 , GLU A:279 , ASP B:275 , TYR C:207 , SER C:208 , ARG C:209BINDING SITE FOR RESIDUE PGE A 901
02AC2SOFTWAREALA A:14 , GLU A:235 , ILE A:236 , ALA A:261BINDING SITE FOR RESIDUE PGE A 902
03AC3SOFTWARELYS A:40 , LYS A:44 , LYS A:247 , TRP A:248 , ARG A:251BINDING SITE FOR RESIDUE FLC A 801
04AC4SOFTWAREARG A:197 , LYS A:203 , LYS A:206 , HOH A:364BINDING SITE FOR RESIDUE PO4 A 287
05AC5SOFTWAREMSE A:80 , ASP A:81 , THR A:82 , ALA A:83 , GLY A:84 , LYS A:85 , GLY A:86BINDING SITE FOR RESIDUE PO4 A 288
06AC6SOFTWARETYR B:207 , ARG B:209 , GLU D:279BINDING SITE FOR RESIDUE PG4 B 1001
07AC7SOFTWAREMSE B:80 , ASP B:81 , THR B:82 , ALA B:83 , GLY B:84 , LYS B:85 , GLY B:86 , ASP B:136 , ARG B:197 , GLN D:99BINDING SITE FOR RESIDUE FLC B 802
08AC8SOFTWAREALA B:14 , ASP B:260BINDING SITE FOR RESIDUE PG4 B 287
09AC9SOFTWAREARG B:197 , LYS B:203 , LYS B:206 , HOH B:363BINDING SITE FOR RESIDUE PO4 B 288
10BC1SOFTWARELYS B:40 , ASN B:245 , LYS B:246 , LYS B:247 , TRP B:248 , HOH B:389BINDING SITE FOR RESIDUE PO4 B 289
11BC2SOFTWAREHIS B:204BINDING SITE FOR RESIDUE CL B 290
12BC3SOFTWAREILE C:178 , GLU C:235 , ILE C:236 , ALA C:261BINDING SITE FOR RESIDUE PG4 C 1001
13BC4SOFTWAREALA C:79 , GLU C:141 , GLU C:214 , TYR C:225BINDING SITE FOR RESIDUE EDO C 901
14BC5SOFTWAREGLN A:99 , ASP C:81 , THR C:82 , LYS C:85 , GLY C:86 , LYS C:107 , ASP C:136 , ARG C:137 , ARG C:197 , HOH C:319 , HOH C:335 , HOH C:338BINDING SITE FOR RESIDUE FLC C 801
15BC6SOFTWAREARG C:197 , LYS C:203 , LYS C:206 , HOH C:325 , HOH C:339 , HOH C:361BINDING SITE FOR RESIDUE PO4 C 287
16BC7SOFTWARELYS C:40 , ASN C:245 , LYS C:246 , LYS C:247 , TRP C:248 , PO4 C:289BINDING SITE FOR RESIDUE PO4 C 288
17BC8SOFTWARELYS C:40 , LYS C:44 , ARG C:251 , PO4 C:288BINDING SITE FOR RESIDUE PO4 C 289
18BC9SOFTWAREASP A:275 , PHE B:274 , GLU B:279 , TYR D:207 , SER D:208 , ARG D:209 , HOH D:532BINDING SITE FOR RESIDUE PG4 D 1002
19CC1SOFTWAREILE D:178 , ILE D:236 , PRO D:238 , ALA D:261BINDING SITE FOR RESIDUE PGE D 901
20CC2SOFTWAREGLN B:99 , ASP D:81 , THR D:82 , LYS D:85 , GLY D:86 , LYS D:107 , ASP D:136 , ARG D:137 , ARG D:197 , HOH D:289 , HOH D:346 , HOH D:354BINDING SITE FOR RESIDUE FLC D 801
21CC3SOFTWAREALA D:79 , ASP D:81 , ARG D:137 , GLU D:141 , LEU D:144 , GLU D:214 , TYR D:225 , HOH D:359BINDING SITE FOR RESIDUE EDO D 287
22CC4SOFTWARELYS D:40 , LYS D:44 , LYS D:247 , TRP D:248 , ARG D:251BINDING SITE FOR RESIDUE PGE D 903
23CC5SOFTWAREARG D:197 , LYS D:203 , LYS D:206 , LYS D:247 , HOH D:331 , HOH D:351BINDING SITE FOR RESIDUE PO4 D 288

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RHF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RHF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RHF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RHF)

(-) Exons   (0, 0)

(no "Exon" information available for 3RHF)

(-) 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:283
 aligned with A1R8G0_PAEAT | A1R8G0 from UniProtKB/TrEMBL  Length:286

    Alignment length:283
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
         A1R8G0_PAEAT     4 VAAVEFAKSPAEVLRVGSGFSLAGVDPESTPGYTGVKADGKALLAAQDARLAELQEKLFAEGKFGNPKRLLLILQAMDTAGKGGIVSHVVGAMDPQGVQLTAFKAPTDEEKSHDFLWRIEKQVPAAGMVGVFDRSQYEDVLIHRVHGWADAAELERRYAAINDFESRLTEQGTTIVKVMLNISKDEQKKRLIARLDDPSKHWKYSRGDLAERAYWDDYMDAYSVAFEKTSTEIAPWHVVPANKKWYARIAVQQLLLDALGGLQLDWPKADFDVAAERALVVES 286
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhh...hhhhhh.......eeeee.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rhf A   4 VAAVEFAKSPAEVLRVGSGFSLAGVDPESTPGYTGVKADGKALLAAQDARLAELQEKLFAEGKFGNPKRLLLILQAmDTAGKGGIVSHVVGAmDPQGVQLTAFKAPTDEEKSHDFLWRIEKQVPAAGmVGVFDRSQYEDVLIHRVHGWADAAELERRYAAINDFESRLTEQGTTIVKVmLNISKDEQKKRLIARLDDPSKHWKYSRGDLAERAYWDDYmDAYSVAFEKTSTEIAPWHVVPANKKWYARIAVQQLLLDALGGLQLDWPKADFDVAAERALVVES 286
                                    13        23        33        43        53        63        73      | 83        93  |    103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
                                                                                                       80-MSE          96-MSE                            131-MSE                                            182-MSE                                 222-MSE                                                            


Chain B from PDB  Type:PROTEIN  Length:281
 aligned with A1R8G0_PAEAT | A1R8G0 from UniProtKB/TrEMBL  Length:286

    Alignment length:281
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 
         A1R8G0_PAEAT     6 AVEFAKSPAEVLRVGSGFSLAGVDPESTPGYTGVKADGKALLAAQDARLAELQEKLFAEGKFGNPKRLLLILQAMDTAGKGGIVSHVVGAMDPQGVQLTAFKAPTDEEKSHDFLWRIEKQVPAAGMVGVFDRSQYEDVLIHRVHGWADAAELERRYAAINDFESRLTEQGTTIVKVMLNISKDEQKKRLIARLDDPSKHWKYSRGDLAERAYWDDYMDAYSVAFEKTSTEIAPWHVVPANKKWYARIAVQQLLLDALGGLQLDWPKADFDVAAERALVVES 286
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh......hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhh...hhhhhh.......eeeee.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rhf B   6 AVEFAKSPAEVLRVGSGFSLAGVDPESTPGYTGVKADGKALLAAQDARLAELQEKLFAEGKFGNPKRLLLILQAmDTAGKGGIVSHVVGAmDPQGVQLTAFKAPTDEEKSHDFLWRIEKQVPAAGmVGVFDRSQYEDVLIHRVHGWADAAELERRYAAINDFESRLTEQGTTIVKVmLNISKDEQKKRLIARLDDPSKHWKYSRGDLAERAYWDDYmDAYSVAFEKTSTEIAPWHVVPANKKWYARIAVQQLLLDALGGLQLDWPKADFDVAAERALVVES 286
                                    15        25        35        45        55        65        75    |   85        95|      105       115       125     | 135       145       155       165       175      |185       195       205       215      |225       235       245       255       265       275       285 
                                                                                                     80-MSE          96-MSE                            131-MSE                                            182-MSE                                 222-MSE                                                            


Chain C from PDB  Type:PROTEIN  Length:281
 aligned with A1R8G0_PAEAT | A1R8G0 from UniProtKB/TrEMBL  Length:286

    Alignment length:281
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 
         A1R8G0_PAEAT     6 AVEFAKSPAEVLRVGSGFSLAGVDPESTPGYTGVKADGKALLAAQDARLAELQEKLFAEGKFGNPKRLLLILQAMDTAGKGGIVSHVVGAMDPQGVQLTAFKAPTDEEKSHDFLWRIEKQVPAAGMVGVFDRSQYEDVLIHRVHGWADAAELERRYAAINDFESRLTEQGTTIVKVMLNISKDEQKKRLIARLDDPSKHWKYSRGDLAERAYWDDYMDAYSVAFEKTSTEIAPWHVVPANKKWYARIAVQQLLLDALGGLQLDWPKADFDVAAERALVVES 286
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh......hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh.eeeee....hhhhhh...hhhhhh.......eeeee.hhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rhf C   6 AVEFAKSPAEVLRVGSGFSLAGVDPESTPGYTGVKADGKALLAAQDARLAELQEKLFAEGKFGNPKRLLLILQAmDTAGKGGIVSHVVGAmDPQGVQLTAFKAPTDEEKSHDFLWRIEKQVPAAGmVGVFDRSQYEDVLIHRVHGWADAAELERRYAAINDFESRLTEQGTTIVKVmLNISKDEQKKRLIARLDDPSKHWKYSRGDLAERAYWDDYmDAYSVAFEKTSTEIAPWHVVPANKKWYARIAVQQLLLDALGGLQLDWPKADFDVAAERALVVES 286
                                    15        25        35        45        55        65        75    |   85        95|      105       115       125     | 135       145       155       165       175      |185       195       205       215      |225       235       245       255       265       275       285 
                                                                                                     80-MSE          96-MSE                            131-MSE                                            182-MSE                                 222-MSE                                                            


Chain D from PDB  Type:PROTEIN  Length:279
 aligned with A1R8G0_PAEAT | A1R8G0 from UniProtKB/TrEMBL  Length:286

    Alignment length:281
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 
         A1R8G0_PAEAT     6 AVEFAKSPAEVLRVGSGFSLAGVDPESTPGYTGVKADGKALLAAQDARLAELQEKLFAEGKFGNPKRLLLILQAMDTAGKGGIVSHVVGAMDPQGVQLTAFKAPTDEEKSHDFLWRIEKQVPAAGMVGVFDRSQYEDVLIHRVHGWADAAELERRYAAINDFESRLTEQGTTIVKVMLNISKDEQKKRLIARLDDPSKHWKYSRGDLAERAYWDDYMDAYSVAFEKTSTEIAPWHVVPANKKWYARIAVQQLLLDALGGLQLDWPKADFDVAAERALVVES 286
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhh.eeeee....hhhhhh...hhhhhh.......eeeee.hhhhhhh....--..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rhf D   6 AVEFAKSPAEVLRVGSGFSLAGVDPESTPGYTGVKADGKALLAAQDARLAELQEKLFAEGKFGNPKRLLLILQAmDTAGKGGIVSHVVGAmDPQGVQLTAFKAPTDEEKSHDFLWRIEKQVPAAGmVGVFDRSQYEDVLIHRV--WADAAELERRYAAINDFESRLTEQGTTIVKVmLNISKDEQKKRLIARLDDPSKHWKYSRGDLAERAYWDDYmDAYSVAFEKTSTEIAPWHVVPANKKWYARIAVQQLLLDALGGLQLDWPKADFDVAAERALVVES 286
                                    15        25        35        45        55        65        75    |   85        95|      105       115       125     | 135       145  |  | 155       165       175      |185       195       205       215      |225       235       245       255       265       275       285 
                                                                                                     80-MSE          96-MSE                            131-MSE          148  |                            182-MSE                                 222-MSE                                                            
                                                                                                                                                                           151
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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 3RHF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RHF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RHF)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A1R8G0_PAEAT | A1R8G0)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0016776    phosphotransferase activity, phosphate group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a phosphate group (acceptor).
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006797    polyphosphate metabolic process    The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid.

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3czp RELATED ID: APC102159 RELATED DB: TARGETDB