3Q3V - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM CAMPYLOBACTER JEJUNI.

Authors :   E. V. Filippova, Z. Wawrzak, O. Onopriyenko, A. Edwards, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)

Date :   22 Dec 10 (Deposition) - 12 Jan 11 (Release) - 09 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Pgk, Converts 3-Phospho-D-Glycerate To 3-Phospho-D- Glyceroyl Phosphate During The Glycolysis Pathway, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zheng, E. V. Filippova, K. L. Tkaczuk, P. Dworzynski, M. Chruszcz, P. J. Porebski, Z. Wawrzak, O. Onopriyenko, M. Kudritska, S. Grimshaw A. Savchenko, W. F. Anderson, W. Minor
Crystal Structures Of Putative Phosphoglycerate Kinases Fro B. Anthracis And C. Jejuni.
J. Struct. Funct. Genom. V. 13 15 2012
PubMed-ID: 22403005 | Reference-DOI: 10.1007/S10969-012-9131-9

Molecule 1 - PHOSPHOGLYCERATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)-MAGIC
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CJ1402C, PGK
	Organism Scientific	:	CAMPYLOBACTER JEJUNI SUBSP. JEJUNI NCTC 11168
	Organism Taxid	:	192222

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 30)

No.	Name	Count	Type	Full Name
1	FMT	4	Ligand/Ion	FORMIC ACID
2	K	4	Ligand/Ion	POTASSIUM ION
3	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
4	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 12)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 14)

No.	Name	Count	Type	Full Name
1	FMT	3	Ligand/Ion	FORMIC ACID
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
4	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:343 , GLY A:345 , GLU A:368 , HOH A:427	BINDING SITE FOR RESIDUE K A 401
02	AC2	SOFTWARE	ALA A:136 , VAL A:139 , HOH A:447 , HOH A:473	BINDING SITE FOR RESIDUE K A 402
03	AC3	SOFTWARE	GLY A:223 , PHE A:227 , PRO A:267 , ASP A:298 , ILE A:299 , MSE A:323 , HOH A:494	BINDING SITE FOR RESIDUE FMT A 403
04	AC4	SOFTWARE	ARG A:64 , ARG A:119 , GLY A:148 , VAL A:149 , HOH A:521	BINDING SITE FOR RESIDUE SO4 A 404
05	AC5	SOFTWARE	ILE A:264 , TYR A:265 , LEU A:266 , VAL A:268 , LEU A:306 , HOH A:481 , TYR B:235 , GLN B:288 , HOH B:432	BINDING SITE FOR RESIDUE PGE A 405
06	AC6	SOFTWARE	SER B:343 , GLY B:345 , GLU B:368 , HOH B:412 , HOH B:501	BINDING SITE FOR RESIDUE K B 401
07	AC7	SOFTWARE	ALA B:136 , VAL B:139 , HOH B:507	BINDING SITE FOR RESIDUE K B 402
08	AC8	SOFTWARE	ALA B:82 , GLU B:88 , ILE B:89 , ASN B:259	BINDING SITE FOR RESIDUE FMT B 403
09	AC9	SOFTWARE	GLY B:223 , ASP B:298 , ILE B:299 , MSE B:323 , HOH B:479	BINDING SITE FOR RESIDUE FMT B 404
10	BC1	SOFTWARE	ILE B:264 , HOH B:517	BINDING SITE FOR RESIDUE FMT B 405
11	BC2	SOFTWARE	HIS B:61 , ARG B:64 , ARG B:119	BINDING SITE FOR RESIDUE SO4 B 406
12	BC3	SOFTWARE	LYS B:177 , ASP B:180	BINDING SITE FOR RESIDUE PGE B 407

(no "SS Bond" information available for 3Q3V)

Asymmetric Unit

No.	Residues
1	Arg A:191	-	Pro A:192
2	Arg B:191	-	Pro B:192

(no "SAP(SNP)/Variant" information available for 3Q3V)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGK_CAMJE	16-26	2	A:16-26 B:16-26

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGK_CAMJE	16-26	1	A:16-26 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGK_CAMJE	16-26	1	- B:16-26

(no "Exon" information available for 3Q3V)

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:394
 aligned with PGK_CAMJE | Q9PMQ5 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:394
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392    
            PGK_CAMJE     3 DIISIKDIDLAKKKVFIRCDFNVPQDDFLNITDDRRIRSAIPTIRYCLDNGCSVILASHLGRPKEISSKYSLEPVAKRLARLLDKEIVMAKDVIGEDAKTKAMNLKAGEILLLENLRFEKGETKNDENLAKELASMVQVYINDAFGVCHRAHSSVEAITKFFDEKHKGAGFLLQKEIDFASNLIKHPARPFVAVVGGSKVSGKLQALTNLLPKVDKLIIGGGMAFTFLKALGYDIGNSLLEEELLEEANKILTKGKNLGVKIYLPVDVVAAPACSQDVPMKFVPAQEIPNGWMGLDIGPASVRLFKEVISDAQTIWWNGPMGVFEIDKFSKGSIKMSHYISEGHATSVVGGGDTADVVARAGDADEMTFISTGGGASLELIEGKELPGVKALRS 396
               SCOP domains d3q3va_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeee...............hhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhh...ee.....hhhhhhhhhhh....eee..hhhhh.hhhhhhhhhhhhhhhh..eeee.hhhhh.......hhhhhhh....eeehhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh....eeee...hhhhhhhhh.........hhhhhhhhhhhhhhhhhh..eee...eeeee.........eeee.hhh....eeeeehhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.hhhhh.ee..hhhhhhhhhh...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PGLYCERATE_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q3v A   3 DIISIKDIDLAKKKVFIRCDFNVPQDDFLNITDDRRIRSAIPTIRYCLDNGCSVILASHLGRPKEISSKYSLEPVAKRLARLLDKEIVmAKDVIGEDAKTKAmNLKAGEILLLENLRFEKGETKNDENLAKELASmVQVYINDAFGVCHRAHSSVEAITKFFDEKHKGAGFLLQKEIDFASNLIKHPARPFVAVVGGSKVSGKLQALTNLLPKVDKLIIGGGmAFTFLKALGYDIGNSLLEEELLEEANKILTKGKNLGVKIYLPVDVVAAPACSQDVPmKFVPAQEIPNGWmGLDIGPASVRLFKEVISDAQTIWWNGPmGVFEIDKFSKGSIKmSHYISEGHATSVVGGGDTADVVARAGDADEmTFISTGGGASLELIEGKELPGVKALRS 396
                                    12        22        32        42        52        62        72        82        92       102  |    112       122       132     | 142       152       162       172       182       192       202       212       222  |    232       242       252       262       272       282       292  |    302       312       322|      332     | 342       352       362      |372       382       392    
                                                                                                                   91-MSE       105-MSE                          138-MSE                                                                                225-MSE                                                  282-MSE      295-MSE                     323-MSE        338-MSE                        369-MSE

Chain B from PDB  Type:PROTEIN  Length:392
 aligned with PGK_CAMJE | Q9PMQ5 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:393
                                    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       293       303       313       323       333       343       353       363       373       383       393   
            PGK_CAMJE     4 IISIKDIDLAKKKVFIRCDFNVPQDDFLNITDDRRIRSAIPTIRYCLDNGCSVILASHLGRPKEISSKYSLEPVAKRLARLLDKEIVMAKDVIGEDAKTKAMNLKAGEILLLENLRFEKGETKNDENLAKELASMVQVYINDAFGVCHRAHSSVEAITKFFDEKHKGAGFLLQKEIDFASNLIKHPARPFVAVVGGSKVSGKLQALTNLLPKVDKLIIGGGMAFTFLKALGYDIGNSLLEEELLEEANKILTKGKNLGVKIYLPVDVVAAPACSQDVPMKFVPAQEIPNGWMGLDIGPASVRLFKEVISDAQTIWWNGPMGVFEIDKFSKGSIKMSHYISEGHATSVVGGGDTADVVARAGDADEMTFISTGGGASLELIEGKELPGVKALRS 396
               SCOP domains d3q3vb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --PGK-3q3vB01 B:6-386                                                                                                                                                                                                                                                                                                                                                                          ---------- Pfam domains (1)
           Pfam domains (2) --PGK-3q3vB02 B:6-386                                                                                                                                                                                                                                                                                                                                                                          ---------- Pfam domains (2)
         Sec.struct. author ..hhhhh.....eeeeee..............hhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhh...ee.....hhhhhhhhhhh....eee..hhhhh.hhhhhhhhhhhhhhhh..eeeeehhhhh.......hhhhhhh....eeehhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhh....eeee...hhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.eee...eeeee.........eeee.hhh....eeeeehhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh......ee...-hhhhhhhh...hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------PGLYCERATE_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q3v B   4 IISIKDIDLAKKKVFIRCDFNVPQDDFLNITDDRRIRSAIPTIRYCLDNGCSVILASHLGRPKEISSKYSLEPVAKRLARLLDKEIVmAKDVIGEDAKTKAmNLKAGEILLLENLRFEKGETKNDENLAKELASmVQVYINDAFGVCHRAHSSVEAITKFFDEKHKGAGFLLQKEIDFASNLIKHPARPFVAVVGGSKVSGKLQALTNLLPKVDKLIIGGGmAFTFLKALGYDIGNSLLEEELLEEANKILTKGKNLGVKIYLPVDVVAAPACSQDVPmKFVPAQEIPNGWmGLDIGPASVRLFKEVISDAQTIWWNGPmGVFEIDKFSKGSIKmSHYISEGHATSVVGGGDTADVVARAGDADEmTFISTG-GASLELIEGKELPGVKALRS 396
                                    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       293 |     303       313       323       333    |  343       353       363     | 373 | |   383       393   
                                                                                                                  91-MSE       105-MSE                          138-MSE                                                                                225-MSE                                                  282-MSE      295-MSE                     323-MSE        338-MSE                        369-MSE75 |                   
                                                                                                                                                                                                                                                                                                                                                                                                               377

Legend:		→ Mismatch	(orange background)
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		→ 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Phosphoglycerate kinase (42)

Superfamily: Phosphoglycerate kinase (42)

Family: automated matches (3)

Protein domain: automated matches (3)

Campylobacter jejuni [TaxId: 192222] (1)

1a	d3q3va_	A:
1b	d3q3vb_	B:

(no "CATH Domain" information available for 3Q3V)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PGK] (23)

Family: PGK (23)

Campylobacter jejuni (1)

1a	PGK-3q3vB01	B:6-386
1b	PGK-3q3vB02	B:6-386

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGK_CAMJE | Q9PMQ5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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.
	GO:0004618	phosphoglycerate kinase activity	Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H(+).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	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.
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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