4BGB - JenaLib

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Title :   NUCLEOTIDE-BOUND CLOSED FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI

Authors :   M. Schacherl, U. Baumann

Date :   24 Mar 13 (Deposition) - 27 Nov 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.34

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

Keywords :   Transferase, Phosphotransfer, Pseudomurein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Schacherl, S. M. Waltersperger, U. Baumann
Structural Characterization Of The Ribonuclease H-Like Type Askha Superfamily Kinase Mk0840 From Methanopyrus Kandleri
Acta Crystallogr. , Sect. D V. 69 2440 2013
PubMed-ID: 24311585 | Reference-DOI: 10.1107/S0907444913022683

Molecule 1 - PUTATIVE SUGAR KINASE MK0840
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 37-358
	Organism Scientific	:	METHANOPYRUS KANDLERI
	Organism Taxid	:	190192
	Other Details	:	DSM6324
	Strain	:	AV19

		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, 18)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CA	1	Ligand/Ion	CALCIUM ION
3	GOL	7	Ligand/Ion	GLYCEROL
4	K	4	Ligand/Ion	POTASSIUM ION
5	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GOL	3	Ligand/Ion	GLYCEROL
4	K	-1	Ligand/Ion	POTASSIUM ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GOL	4	Ligand/Ion	GLYCEROL
4	K	-1	Ligand/Ion	POTASSIUM ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:48 , GLY A:167 , THR A:191 , ASP A:195 , TYR A:206 , ASP A:207 , GLU A:208 , GLY A:209 , GLY A:298 , GLY A:299 , LYS A:301 , GOL A:1355 , HOH A:2125 , HOH A:2182 , HOH A:2201 , HOH A:2203 , HOH A:2221	BINDING SITE FOR RESIDUE ADP A1352
02	AC2	SOFTWARE	ASN B:47 , THR B:48 , GLY B:49 , GLY B:167 , ALA B:168 , THR B:191 , ASP B:195 , TYR B:206 , ASP B:207 , GLU B:208 , GLY B:209 , GLY B:298 , GLY B:299 , LYS B:301 , GOL B:1356 , MG B:1359 , MG B:1360 , HOH B:2006 , HOH B:2134 , HOH B:2151 , HOH B:2245 , HOH B:2293	BINDING SITE FOR RESIDUE ADP B1352
03	AC3	SOFTWARE	ALA B:142 , PRO B:143 , ASP B:144 , ASP B:146 , VAL B:171 , HOH B:2134	BINDING SITE FOR RESIDUE GOL B1353
04	AC4	SOFTWARE	ALA A:142 , PRO A:143 , ASP A:144 , ASP A:146 , ALA A:147 , HOH A:2083 , HOH A:2224 , HOH A:2225	BINDING SITE FOR RESIDUE GOL A1353
05	AC5	SOFTWARE	GLU B:200 , GLU B:252 , ARG B:256 , ARG B:307 , ARG B:308 , GLU B:311 , HOH B:2214 , HOH B:2294	BINDING SITE FOR RESIDUE GOL B1354
06	AC6	SOFTWARE	THR A:50 , TYR A:52 , GLU A:67 , GLU A:68 , GLY A:69 , ARG A:98	BINDING SITE FOR RESIDUE GOL A1354
07	AC7	SOFTWARE	GLN A:44 , GLY A:49 , ASP A:51 , ARG A:66 , GLU A:323 , GLU A:326 , ADP A:1352 , CA A:1359 , HOH A:2006 , HOH A:2202	BINDING SITE FOR RESIDUE GOL A1355
08	AC8	SOFTWARE	GLY B:72 , GLU B:82 , GLU B:215 , GLU B:217 , MG B:1361 , HOH B:2042 , HOH B:2171 , HOH B:2172	BINDING SITE FOR RESIDUE GOL B1355
09	AC9	SOFTWARE	GLN B:44 , GLY B:49 , ASP B:51 , ADP B:1352 , MG B:1360 , HOH B:2004 , HOH B:2015	BINDING SITE FOR RESIDUE GOL B1356
10	BC1	SOFTWARE	ASP B:114 , ASP B:138 , GLY B:141 , PRO B:143 , ASP B:144 , HOH B:2095 , HOH B:2117	BINDING SITE FOR RESIDUE K B1357
11	BC2	SOFTWARE	ASP B:138 , ALA B:142 , PHE B:182 , GLY B:183 , ALA B:185 , SER B:243	BINDING SITE FOR RESIDUE K B1358
12	BC3	SOFTWARE	ASP A:138 , ALA A:142 , PHE A:182 , GLY A:183 , ALA A:185 , SER A:243 , HOH A:2143	BINDING SITE FOR RESIDUE K A1356
13	BC4	SOFTWARE	GLY A:141 , ASP A:144 , HOH A:2084 , HOH A:2100 , ARG B:88	BINDING SITE FOR RESIDUE K A1357
14	BC5	SOFTWARE	ASP A:165 , HOH A:2102 , HOH A:2123 , HOH A:2125 , HOH A:2127 , HOH A:2202	BINDING SITE FOR RESIDUE MG A1358
15	BC6	SOFTWARE	ASP B:165 , ADP B:1352 , HOH B:2005 , HOH B:2132	BINDING SITE FOR RESIDUE MG B1359
16	BC7	SOFTWARE	ADP B:1352 , GOL B:1356 , HOH B:2004 , HOH B:2012 , HOH B:2014 , HOH B:2015	BINDING SITE FOR RESIDUE MG B1360
17	BC8	SOFTWARE	GLY B:72 , GLU B:215 , GOL B:1355 , HOH B:2172	BINDING SITE FOR RESIDUE MG B1361
18	BC9	SOFTWARE	GLU A:323 , GLU A:326 , GOL A:1355 , HOH A:2198 , HOH A:2201 , HOH A:2203	BINDING SITE FOR RESIDUE CA A1359

(no "SS Bond" information available for 4BGB)

Asymmetric Unit

No.	Residues
1	Ala A:142	-	Pro A:143
2	Ala B:142	-	Pro B:143

(no "SAP(SNP)/Variant" information available for 4BGB)

(no "PROSITE Motif" information available for 4BGB)

(no "Exon" information available for 4BGB)

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
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Chain A from PDB  Type:PROTEIN  Length:316
 aligned with Q8TX37_METKA | Q8TX37 from UniProtKB/TrEMBL  Length:358

    Alignment length:316
                                    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       295       305       315       325       335       345      
         Q8TX37_METKA    36 TLTRVLGIQLGNTGTDYCVMNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPMIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAMAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDMDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEGG 351
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeeeeee....eeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhh....eeeeee..eeeeeeee..ee.....eeee.hhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhh.ee..ee...........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bgb A  36 HLTRVLGIQLGNTGTDYCVMNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPMIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAMAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDMDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEGG 351
                                    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       295       305       315       325       335       345

Chain B from PDB  Type:PROTEIN  Length:315
 aligned with Q8TX37_METKA | Q8TX37 from UniProtKB/TrEMBL  Length:358

    Alignment length:315
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346     
         Q8TX37_METKA    37 LTRVLGIQLGNTGTDYCVMNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPMIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAMAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDMDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEGG 351
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeeee....eeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhh....eeeeee..eeeeeeee..ee.....eeee.hhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhh.ee..ee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bgb B  37 LTRVLGIQLGNTGTDYCVMNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPMIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAMAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDMDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEGG 351
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346

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 '\|'

(no "SCOP Domain" information available for 4BGB)

(no "CATH Domain" information available for 4BGB)

(no "Pfam Domain" information available for 4BGB)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8TX37_METKA | Q8TX37)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
biological process
	GO:0006040	amino sugar metabolic process	The chemical reactions and pathways involving any amino sugar, sugars containing an amino group in place of a hydroxyl group.
	GO:0009254	peptidoglycan turnover	The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:142 - Pro A:143	[ RasMol ]
		Ala B:142 - Pro B:143	[ RasMol ]

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	4bgb
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	Q8TX37_METKA \| Q8TX37	:	4bg8 4bg9 4bga

4bg8	APO FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI (MONOCLINIC SPACE GROUP)
4bg9	APO FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI (ORTHORHOMBIC SPACE GROUP)
4bga	NUCLEOTIDE-BOUND OPEN FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (5, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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