2AP1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE PUTATIVE REGULATORY PROTEIN

Authors :   J. S. Brunzelle, G. Minasov, L. Shuvalova, F. R. Collart, A. Joachimiak W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)

Date :   15 Aug 05 (Deposition) - 27 Sep 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Zinc Binding Protein, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Putative Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Brunzelle, G. Minasov, L. Shuvalova, F. R. Collart, W. F. Anderso
Crystal Structure Of The Putative Regulatory Protein
To Be Published
PubMed: search

Molecule 1 - PUTATIVE REGULATOR PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	YCFX
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	NA	1	Ligand/Ion	SODIUM ION
2	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:157 , CYS A:177 , CYS A:179 , CYS A:184	BINDING SITE FOR RESIDUE ZN A 304
2	AC2	SOFTWARE	HOH A:334 , HOH A:358 , HOH A:364 , HOH A:383 , HOH A:390 , HOH A:506	BINDING SITE FOR RESIDUE NA A 305

(no "SS Bond" information available for 2AP1)

(no "Cis Peptide Bond" information available for 2AP1)

(no "SAP(SNP)/Variant" information available for 2AP1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ROK	PS01125	ROK family signature.	NAGK_SALTY	130-157	1	A:130-157

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ROK	PS01125	ROK family signature.	NAGK_SALTY	130-157	1	A:130-157

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ROK	PS01125	ROK family signature.	NAGK_SALTY	130-157	2	A:130-157

(no "Exon" information available for 2AP1)

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:305
 aligned with NAGK_SALTY | Q8ZPZ9 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:305
                              1                                                                                                                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     
           NAGK_SALTY     - --MYYGFDIGGTKIALGVFDSTRRLQWEKRVPTPHTSYSAFLDAVCELVEEADQRFGVKGSVGIGIPGMPETEDGTLYAANVPAASGKPLRADLSARLDRDVRLDNDANCFALSEAWDDEFTQYPLVMGLILGTGVGGGLVLNGKPITGQSYITGEFGHMRLPVDALTLMGFDFPLRRCGCGQMGCIENYLSGRGFAWLYQHYYDQSLQAPEIIALWEQGDEQAHAHVERYLDLLAVCLGNILTIVDPDLLVIGGGLSNFTAITTQLAERLPRHLLPVARAPRIERARHGDAGGMRGAAFLHLTD 303
               SCOP domains --d2ap1a2 A:1-117 Putative regulator protein YcfX                                                                      d2ap1a1 A:118-303 Putative regulator protein YcfX                                                                                                                                          SCOP domains
               CATH domains 2ap1A01 A:-1-118,A:285-303  [code=3.30.420.40, no name defined]                                                         2ap1A02 A:119-284  [code=3.30.420.40, no name defined]                                                                                                                2ap1A01             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeee......................hhhhhhhhhhh..eeeeehhhhhhhhhhh..hhhhh.eeeeeee...eeeeeee..eee........hhhhh..hhhhhhhhh...............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------ROK  PDB: A:130-157         -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ap1 A  -1 NAMYYGFDIGGTKIALGVFDSTRRLQWEKRVPTPHTSYSAFLDAVCELVEEADQRFGVKGSVGIGIPGMPETEDGTLYAANVPAASGKPLRADLSARLDRDVRLDNDANCFALSEAWDDEFTQYPLVMGLILGTGVGGGLVLNGKPITGQSYITGEFGHMRLPVDALTLMGFDFPLRRCGCGQMGCIENYLSGRGFAWLYQHYYDQSLQAPEIIALWEQGDEQAHAHVERYLDLLAVCLGNILTIVDPDLLVIGGGLSNFTAITTQLAERLPRHLLPVARAPRIERARHGDAGGMRGAAFLHLTD 303
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: ROK (11)

Protein domain: Putative regulator protein YcfX (1)

Salmonella typhimurium [TaxId: 90371] (1)

1a	d2ap1a1	A:118-303
1b	d2ap1a2	A:1-117

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.40, no name defined] (217)

Salmonella typhimurium. Organism_taxid: 602. (3)

1a	2ap1A01	A:-1-118,A:285-303
1b	2ap1A02	A:119-284

(no "Pfam Domain" information available for 2AP1)

Asymmetric Unit(hide GO term definitions)

Chain A (NAGK_SALTY | Q8ZPZ9)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0045127	N-acetylglucosamine kinase activity	Catalysis of the reaction: N-acetyl-D-glucosamine + ATP = N-acetyl-D-glucosamine 6-phosphate + ADP + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006044	N-acetylglucosamine metabolic process	The chemical reactions and pathways involving N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0046835	carbohydrate phosphorylation	The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
	GO:0009254	peptidoglycan turnover	The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
	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.

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