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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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:	A	B	C	D
Biological Unit 3 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (7, 43)

Asymmetric Unit (7, 43)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	FLC	4	Ligand/Ion	CITRATE ANION
4	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
5	PG4	4	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL
7	PO4	8	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (6, 21)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	FLC	2	Ligand/Ion	CITRATE ANION
4	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
5	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
7	PO4	5	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (6, 42)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	FLC	4	Ligand/Ion	CITRATE ANION
4	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
5	PG4	4	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL
7	PO4	8	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (6, 21)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	FLC	2	Ligand/Ion	CITRATE ANION
4	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
5	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
7	PO4	3	Ligand/Ion	PHOSPHATE ION

Sites (23, 23)

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:274 , GLU A:279 , ASP B:275 , TYR C:207 , SER C:208 , ARG C:209	BINDING SITE FOR RESIDUE PGE A 901
02	AC2	SOFTWARE	ALA A:14 , GLU A:235 , ILE A:236 , ALA A:261	BINDING SITE FOR RESIDUE PGE A 902
03	AC3	SOFTWARE	LYS A:40 , LYS A:44 , LYS A:247 , TRP A:248 , ARG A:251	BINDING SITE FOR RESIDUE FLC A 801
04	AC4	SOFTWARE	ARG A:197 , LYS A:203 , LYS A:206 , HOH A:364	BINDING SITE FOR RESIDUE PO4 A 287
05	AC5	SOFTWARE	MSE A:80 , ASP A:81 , THR A:82 , ALA A:83 , GLY A:84 , LYS A:85 , GLY A:86	BINDING SITE FOR RESIDUE PO4 A 288
06	AC6	SOFTWARE	TYR B:207 , ARG B:209 , GLU D:279	BINDING SITE FOR RESIDUE PG4 B 1001
07	AC7	SOFTWARE	MSE 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:99	BINDING SITE FOR RESIDUE FLC B 802
08	AC8	SOFTWARE	ALA B:14 , ASP B:260	BINDING SITE FOR RESIDUE PG4 B 287
09	AC9	SOFTWARE	ARG B:197 , LYS B:203 , LYS B:206 , HOH B:363	BINDING SITE FOR RESIDUE PO4 B 288
10	BC1	SOFTWARE	LYS B:40 , ASN B:245 , LYS B:246 , LYS B:247 , TRP B:248 , HOH B:389	BINDING SITE FOR RESIDUE PO4 B 289
11	BC2	SOFTWARE	HIS B:204	BINDING SITE FOR RESIDUE CL B 290
12	BC3	SOFTWARE	ILE C:178 , GLU C:235 , ILE C:236 , ALA C:261	BINDING SITE FOR RESIDUE PG4 C 1001
13	BC4	SOFTWARE	ALA C:79 , GLU C:141 , GLU C:214 , TYR C:225	BINDING SITE FOR RESIDUE EDO C 901
14	BC5	SOFTWARE	GLN 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:338	BINDING SITE FOR RESIDUE FLC C 801
15	BC6	SOFTWARE	ARG C:197 , LYS C:203 , LYS C:206 , HOH C:325 , HOH C:339 , HOH C:361	BINDING SITE FOR RESIDUE PO4 C 287
16	BC7	SOFTWARE	LYS C:40 , ASN C:245 , LYS C:246 , LYS C:247 , TRP C:248 , PO4 C:289	BINDING SITE FOR RESIDUE PO4 C 288
17	BC8	SOFTWARE	LYS C:40 , LYS C:44 , ARG C:251 , PO4 C:288	BINDING SITE FOR RESIDUE PO4 C 289
18	BC9	SOFTWARE	ASP A:275 , PHE B:274 , GLU B:279 , TYR D:207 , SER D:208 , ARG D:209 , HOH D:532	BINDING SITE FOR RESIDUE PG4 D 1002
19	CC1	SOFTWARE	ILE D:178 , ILE D:236 , PRO D:238 , ALA D:261	BINDING SITE FOR RESIDUE PGE D 901
20	CC2	SOFTWARE	GLN 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:354	BINDING SITE FOR RESIDUE FLC D 801
21	CC3	SOFTWARE	ALA D:79 , ASP D:81 , ARG D:137 , GLU D:141 , LEU D:144 , GLU D:214 , TYR D:225 , HOH D:359	BINDING SITE FOR RESIDUE EDO D 287
22	CC4	SOFTWARE	LYS D:40 , LYS D:44 , LYS D:247 , TRP D:248 , ARG D:251	BINDING SITE FOR RESIDUE PGE D 903
23	CC5	SOFTWARE	ARG D:197 , LYS D:203 , LYS D:206 , LYS D:247 , HOH D:331 , HOH D:351	BINDING SITE FOR RESIDUE PO4 D 288

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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Description