3KZF - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF GIARDIA CARBAMATE KINASE

Authors :   A. Galkin, O. Herzberg

Date :   08 Dec 09 (Deposition) - 07 Apr 10 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Carbamate Kinase, Arginine Dihydrolase Pathway, Giardia Lamblia, Drug Target, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Galkin, L. Kulakova, R. Wu, T. E. Nash, D. Dunaway-Mariano, O. Herzberg
X-Ray Structure And Characterization Of Carbamate Kinase From The Human Parasite Giardia Lamblia.
Acta Crystallogr. , Sect. F V. 66 386 2010
PubMed-ID: 20383005 | Reference-DOI: 10.1107/S1744309110004665

Molecule 1 - CARBAMATE KINASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PDEST-HISMBP
	Gene	:	CK, GL50803_16453
	Organism Scientific	:	GIARDIA LAMBLIA ATCC 50803
	Organism Taxid	:	184922
	Strain	:	WB

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:13 , GLY B:56 , LYS B:216	BINDING SITE FOR RESIDUE GOL B 321
2	AC2	SOFTWARE	GLY D:12 , GLY D:13 , LYS D:131	BINDING SITE FOR RESIDUE GOL D 322
3	AC3	SOFTWARE	GLY C:13	BINDING SITE FOR RESIDUE GOL C 323
4	AC4	SOFTWARE	GLY A:13 , LYS A:278	BINDING SITE FOR RESIDUE GOL A 324

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

Asymmetric Unit

No.	Residues
1	Lys A:22	-	Gly A:23
2	Pro A:248	-	Asp A:249
3	Thr B:138	-	Glu B:139
4	Glu C:21	-	Lys C:22
5	Ala C:272	-	Gly C:273
6	Gly D:71	-	Val D:72
7	Gly D:273	-	Ser D:274

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

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

(no "Exon" information available for 3KZF)

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:285
 aligned with A8BB85_GIAIC | A8BB85 from UniProtKB/TrEMBL  Length:316

    Alignment length:315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311     
         A8BB85_GIAIC     2 SAGKTVVIALGGNAMLQAKEKGDYDTQRKNVEIAASEIYKIHKAGYKVVLTSGNGPQVGAIKLQNQAAAGVSPEMPLHVCGAMSQGFIGYMMSQAMDNVFCANNEPANCVTCVTQTLVDPKDQAFTNPTKPVGRFYTEQEAKDLMAANPGKILREDAGRGWRVVVPSPRPLEIVEYGVIKTLIDNNVLVICTNGGGIPCKRENKVISGVDAVIDKDLATSLLAKTLNSDYLMILTDVLNACINYKKPDERKLEEIKLSEILALEKDGHFAAGSMGPKVRAAIEFTQATGKMSIITSLSTAVDALNGKCGTRIIKD 316
               SCOP domains d3kzfa_ A: autom  ated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3kzfA00 A:2-316    [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......--....hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eeee...hhhhh...ee..--------------------------....ee....eeee.hhhhhhhhhhh..eee.hhhhheeeee....eee.....hhhhhhhhhhhhhh...eee.......ee.......ee..eeehhhhhhhhh.....--.hhhhhhhhhhhhhhhh..eee.hhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kzf A   2 SAGKTVVIALGGNAML--KEKGDYDTQRKNVEIAASEIYKIHKAGYKVVLTSGNGPQVGAIKLQNQAAAGVSPEMPLHVCGAMSQGFIGYMMSQAMDNVFCANNEPANCVTCVTQTLVDPKDQAFTNPTKPVG--------------------------GWRVVVPSPRPLEIVEYGVIKTLIDNNVLVICTNGGGIPCKRENKVISGVDAVIDKDLATSLLAKTLNSDYLMILTDVLNACINYKKPDERKLEEIKLSEILALEKDGHFA--SMGPKVRAAIEFTQATGKMSIITSLSTAVDALNGKCGTRIIKD 316
                                    11     |  21        31        41        51        61        71        81        91       101       111       121       131  |      -         -       161       171       181       191       201       211       221       231       241       251       261       271  |    281       291       301       311     
                                          17 20                                                                                                               134                        161                                                                                                           271  |                                          
                                                                                                                                                                                                                                                                                                          274

Chain B from PDB  Type:PROTEIN  Length:298
 aligned with A8BB85_GIAIC | A8BB85 from UniProtKB/TrEMBL  Length:316

    Alignment length:315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311     
         A8BB85_GIAIC     2 SAGKTVVIALGGNAMLQAKEKGDYDTQRKNVEIAASEIYKIHKAGYKVVLTSGNGPQVGAIKLQNQAAAGVSPEMPLHVCGAMSQGFIGYMMSQAMDNVFCANNEPANCVTCVTQTLVDPKDQAFTNPTKPVGRFYTEQEAKDLMAANPGKILREDAGRGWRVVVPSPRPLEIVEYGVIKTLIDNNVLVICTNGGGIPCKRENKVISGVDAVIDKDLATSLLAKTLNSDYLMILTDVLNACINYKKPDERKLEEIKLSEILALEKDGHFAAGSMGPKVRAAIEFTQATGKMSIITSLSTAVDALNGKCGTRIIKD 316
               SCOP domains d3kzfb_ B: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3kzfB00 B:2-316  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhh.......hhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eee....hhhhhh..eee......-------------...........eee......ee.hhhhhhhhhhh..eee.hhhhheeee......ee.....hhhhhhhhhhhhhh..eeeeee.......--..........eehhhhhhhhhh...--..hhhhhhhhhhhhhhhh.eeeeee..hhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kzf B   2 SAGKTVVIALGGNAMLQAKEKGDYDTQRKNVEIAASEIYKIHKAGYKVVLTSGNGPQVGAIKLQNQAAAGVSPEMPLHVCGAMSQGFIGYMMSQAMDNVFCANNEPANCVTCVTQTLVDPKDQAFTNPTKPVGRFYTE-------------ILREDAGRGWRVVVPSPRPLEIVEYGVIKTLIDNNVLVICTNGGGIPCKRENKVISGVDAVIDKDLATSLLAKTLNSDYLMILTDVLNACI--KKPDERKLEEIKLSEILALEKDGHF--GSMGPKVRAAIEFTQATGKMSIITSLSTAVDALNGKCGTRIIKD 316
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       | -         - |     161       171       181       191       201       211       221       231       241 |  |  251       261        |- |     281       291       301       311     
                                                                                                                                                                   139           153                                                                                       243  |                     270  |                                           
                                                                                                                                                                                                                                                                              246                        273

Chain C from PDB  Type:PROTEIN  Length:287
 aligned with A8BB85_GIAIC | A8BB85 from UniProtKB/TrEMBL  Length:316

    Alignment length:315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311     
         A8BB85_GIAIC     2 SAGKTVVIALGGNAMLQAKEKGDYDTQRKNVEIAASEIYKIHKAGYKVVLTSGNGPQVGAIKLQNQAAAGVSPEMPLHVCGAMSQGFIGYMMSQAMDNVFCANNEPANCVTCVTQTLVDPKDQAFTNPTKPVGRFYTEQEAKDLMAANPGKILREDAGRGWRVVVPSPRPLEIVEYGVIKTLIDNNVLVICTNGGGIPCKRENKVISGVDAVIDKDLATSLLAKTLNSDYLMILTDVLNACINYKKPDERKLEEIKLSEILALEKDGHFAAGSMGPKVRAAIEFTQATGKMSIITSLSTAVDALNGKCGTRIIKD 316
               SCOP domains d3kzfc_ C: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3kzfC00 C:2-316  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee............hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...eee....hhhhhh..ee.....------------------------...ee......ee.hhhhhhhhhhh..eee.hhhhheeee......ee.....hhhhhhhhhhhhh...eeeeee....ee....----.ee.eeehhhhhhhhh.......hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kzf C   2 SAGKTVVIALGGNAMLQAKEKGDYDTQRKNVEIAASEIYKIHKAGYKVVLTSGNGPQVGAIKLQNQAAAGVSPEMPLHVCGAMSQGFIGYMMSQAMDNVFCANNEPANCVTCVTQTLVDPKDQAFTNPTKPVGRFY------------------------WRVVVPSPRPLEIVEYGVIKTLIDNNVLVICTNGGGIPCKRENKVISGVDAVIDKDLATSLLAKTLNSDYLMILTDVLNACINYK----RKLEEIKLSEILALEKDGHFAAGSMGPKVRAAIEFTQATGKMSIITSLSTAVDALNGKCGTRIIKD 316
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     |   -         -         -|      171       181       191       201       211       221       231       241    |  251       261       271       281       291       301       311     
                                                                                                                                                                 137                      162                                                                                 246  251

Chain D from PDB  Type:PROTEIN  Length:293
 aligned with A8BB85_GIAIC | A8BB85 from UniProtKB/TrEMBL  Length:316

    Alignment length:315
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311     
         A8BB85_GIAIC     2 SAGKTVVIALGGNAMLQAKEKGDYDTQRKNVEIAASEIYKIHKAGYKVVLTSGNGPQVGAIKLQNQAAAGVSPEMPLHVCGAMSQGFIGYMMSQAMDNVFCANNEPANCVTCVTQTLVDPKDQAFTNPTKPVGRFYTEQEAKDLMAANPGKILREDAGRGWRVVVPSPRPLEIVEYGVIKTLIDNNVLVICTNGGGIPCKRENKVISGVDAVIDKDLATSLLAKTLNSDYLMILTDVLNACINYKKPDERKLEEIKLSEILALEKDGHFAAGSMGPKVRAAIEFTQATGKMSIITSLSTAVDALNGKCGTRIIKD 316
               SCOP domains d3kzfd_ D: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 3kzfD00 D:2-316  [code=3.40.1160.10, no name defined]                                                                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) ---AA_kinase-3kzfD01 D:5-297                                                                                                                                                                                                                                                                            ------------------- Pfam domains (1)
           Pfam domains (2) ---AA_kinase-3kzfD02 D:5-297                                                                                                                                                                                                                                                                            ------------------- Pfam domains (2)
           Pfam domains (3) ---AA_kinase-3kzfD03 D:5-297                                                                                                                                                                                                                                                                            ------------------- Pfam domains (3)
           Pfam domains (4) ---AA_kinase-3kzfD04 D:5-297                                                                                                                                                                                                                                                                            ------------------- Pfam domains (4)
         Sec.struct. author ....eeeeee............hhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..eee....hhhhh...ee.......-------------..ee......eeee......ee.hhhhhhhhhhh..eeee.hhhheeee......ee.....hhhhhhhhhhhhhh..eeeeee......-------.......hhhhhhhhhhh...--...hhhhhhhhhhhhhhh.eeeeee..hhhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kzf D   2 SAGKTVVIALGGNAMLQAKEKGDYDTQRKNVEIAASEIYKIHKAGYKVVLTSGNGPQVGAIKLQNQAAAGVSPEMPLHVCGAMSQGFIGYMMSQAMDNVFCANNEPANCVTCVTQTLVDPKDQAFTNPTKPVGRFYTE-------------ILREDAGRGWRVVVPSPRPLEIVEYGVIKTLIDNNVLVICTNGGGIPCKRENKVISGVDAVIDKDLATSLLAKTLNSDYLMILTDVLNAC-------ERKLEEIKLSEILALEKDGHF--GSMGPKVRAAIEFTQATGKMSIITSLSTAVDALNGKCGTRIIKD 316
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       | -         - |     161       171       181       191       201       211       221       231       241|      251       261        |- |     281       291       301       311     
                                                                                                                                                                   139           153                                                                                      242     250                 270  |                                           
                                                                                                                                                                                                                                                                                                         273

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: Carbamate kinase-like (63)

Superfamily: Carbamate kinase-like (63)

Family: automated matches (24)

Protein domain: automated matches (24)

Giardia lamblia [TaxId: 184922] (5)

1a	d3kzfa_	A:
1b	d3kzfb_	B:
1c	d3kzfc_	C:
1d	d3kzfd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Carbamate kinase (24)

Homologous Superfamily: [code=3.40.1160.10, no name defined] (24)

Giardia lamblia atcc 50803. Organism_taxid: 184922. Strain: wb. (1)

1a	3kzfA00	A:2-316
1b	3kzfC00	C:2-316
1c	3kzfD00	D:2-316
1d	3kzfB00	B:2-316

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: AA_kinase] (20)

Family: AA_kinase (20)

Giardia intestinalis (strain ATCC 50803 / WB clone C6) (Giardia lamblia) (1)

1a	AA_kinase-3kzfD01	D:5-297
1b	AA_kinase-3kzfD02	D:5-297
1c	AA_kinase-3kzfD03	D:5-297
1d	AA_kinase-3kzfD04	D:5-297

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (A8BB85_GIAIC | A8BB85)

molecular function
	GO:0008804	carbamate kinase activity	Catalysis of the reaction: ATP + NH3 + CO2 = ADP + carbamoyl phosphate.
	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: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:0019546	arginine deiminase pathway	The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine and CO2, using the enzyme arginine deiminase.
	GO:0006525	arginine metabolic process	The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala C:272 - Gly C:273	[ RasMol ]
		Glu C:21 - Lys C:22	[ RasMol ]
		Gly D:273 - Ser D:274	[ RasMol ]
		Gly D:71 - Val D:72	[ RasMol ]
		Lys A:22 - Gly A:23	[ RasMol ]
		Pro A:248 - Asp A:249	[ RasMol ]
		Thr B:138 - Glu B:139	[ RasMol ]

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	A8BB85_GIAIC \| A8BB85	:	4jz7 4jz8 4jz9 4olc

(no "Related Entries Specified in the PDB File" available for 3KZF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

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