3L0S - JenaLib

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Title :   CRYSTAL STRUCTURES OF ZINC, COBALT AND IRON CONTAINING ADENYLATE KINASE FROM GRAM-NEGATIVE BACTERIA DESULFOVIBRIO GIGAS

Authors :   A. Mukhopadhyay, J. Trincao, M. J. Romao

Date :   10 Dec 09 (Deposition) - 15 Dec 10 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Adenylate Kinase, Gram-Negative, Cobalt, Atp-Binding, Kinase, Nucleotide-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Mukhopadhyay, A. V. Kladova, S. A. Bursakov, O. Y. Gavel, J. J. Calvete, V. L. Shnyrov, I. Moura, J. J. G. Moura, M. J. Romao, J. Trincao
Crystal Structure Of The Zinc-, Cobalt-, And Iron-Containin Adenylate Kinase From Desulfovibrio Gigas: A Novel Metal-Containing Adenylate Kinase From Gram-Negative Bacteria
J. Biol. Inorg. Chem. V. 16 51 2011
PubMed-ID: 20821240 | Reference-DOI: 10.1007/S00775-010-0700-8

Molecule 1 - ADENYLATE KINASE
	Chains	:	A, C
	EC Number	:	2.7.4.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	DESULFOVIBRIO GIGAS
	Organism Taxid	:	879

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CO	2	Ligand/Ion	COBALT (II) ION
2	TAR	2	Ligand/Ion	D(-)-TARTARIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	TAR	1	Ligand/Ion	D(-)-TARTARIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	TAR	1	Ligand/Ion	D(-)-TARTARIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:129 , HIS A:135 , CYS A:151 , CYS A:154	BINDING SITE FOR RESIDUE CO A 224
2	AC2	SOFTWARE	PRO A:8 , ASN A:9 , GLY A:10 , SER A:11 , GLY A:12 , LYS A:13 , ARG A:126 , HOH A:417 , HOH A:440 , HOH A:482 , HOH A:499 , ASN C:131 , ASN C:132 , HOH C:243	BINDING SITE FOR RESIDUE TAR A 225
3	AC3	SOFTWARE	CYS C:129 , HIS C:135 , CYS C:151 , CYS C:154	BINDING SITE FOR RESIDUE CO C 224
4	AC4	SOFTWARE	ASN A:131 , ASN A:132 , PRO C:8 , ASN C:9 , GLY C:10 , SER C:11 , GLY C:12 , LYS C:13 , GLY C:14 , ARG C:126 , HOH C:293 , HOH C:308 , HOH C:416 , HOH C:428	BINDING SITE FOR RESIDUE TAR C 225

(no "SS Bond" information available for 3L0S)

Asymmetric Unit

No.	Residues
1	Phe A:85	-	Pro A:86
2	Phe C:85	-	Pro C:86

(no "SAP(SNP)/Variant" information available for 3L0S)

(no "PROSITE Motif" information available for 3L0S)

(no "Exon" information available for 3L0S)

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:223
 aligned with C7U112_DESGI | C7U112 from UniProtKB/TrEMBL  Length:223

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         C7U112_DESGI     1 MNILIFGPNGSGKGTQGNLVKDKYSLAHIESGGIFREHIGGGTELGKKAKEFIDRGDLVPDDITIPMVLETLESKGKDGWLLDGFPRNTVQAQKLFEALQEKGMKINFVIEILLPREVAKNRIMGRRICKNNPNHPNNIFIEAIKPNGDVCRVCGGALSARADDQDEGAINKRHDIYYNTVDGTLAAAYYYKNMAAKEGFVYIELDGEGSIDSIKDTLLAQLA 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhh...eeeehhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh..ee...........hhhhh............ee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0s A   1 MNILIFGPNGSGKGTQGNLVKDKYSLAHIESGGIFREHIGGGTELGKKAKEFIDRGDLVPDDITIPMVLETLESKGKDGWLLDGFPRNTVQAQKLFEALQEKGMKINFVIEILLPREVAKNRIMGRRICKNNPNHPNNIFIEAIKPNGDVCRVCGGALSARADDQDEGAINKRHDIYYNTVDGTLAAAYYYKNMAAKEGFVYIELDGEGSIDSIKDTLLAQLA 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:223
 aligned with C7U112_DESGI | C7U112 from UniProtKB/TrEMBL  Length:223

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         C7U112_DESGI     1 MNILIFGPNGSGKGTQGNLVKDKYSLAHIESGGIFREHIGGGTELGKKAKEFIDRGDLVPDDITIPMVLETLESKGKDGWLLDGFPRNTVQAQKLFEALQEKGMKINFVIEILLPREVAKNRIMGRRICKNNPNHPNNIFIEAIKPNGDVCRVCGGALSARADDQDEGAINKRHDIYYNTVDGTLAAAYYYKNMAAKEGFVYIELDGEGSIDSIKDTLLAQLA 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----ADK-3l0sC01 C:5-195                                                                                                                                                                            ---------------------------- Pfam domains (1)
           Pfam domains (2) ----ADK-3l0sC02 C:5-195                                                                                                                                                                            ---------------------------- Pfam domains (2)
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhheeee.......ee..hhhhh............ee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0s C   1 MNILIFGPNGSGKGTQGNLVKDKYSLAHIESGGIFREHIGGGTELGKKAKEFIDRGDLVPDDITIPMVLETLESKGKDGWLLDGFPRNTVQAQKLFEALQEKGMKINFVIEILLPREVAKNRIMGRRICKNNPNHPNNIFIEAIKPNGDVCRVCGGALSARADDQDEGAINKRHDIYYNTVDGTLAAAYYYKNMAAKEGFVYIELDGEGSIDSIKDTLLAQLA 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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 3L0S)

(no "CATH Domain" information available for 3L0S)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: ADK (22)

Desulfovibrio gigas (3)

1a	ADK-3l0sC01	C:5-195
1b	ADK-3l0sC02	C:5-195

Asymmetric Unit(hide GO term definitions)

Chain A,C (C7U112_DESGI | C7U112)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004017	adenylate kinase activity	Catalysis of the reaction: ATP + AMP = 2 ADP.
	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:0019205	nucleobase-containing compound kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate.
	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.
biological process
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0046939	nucleotide phosphorylation	The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:85 - Pro A:86	[ RasMol ]
		Phe C:85 - Pro C:86	[ RasMol ]

Biological Units
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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