1VCO - JenaLib

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Title :   CRYSTAL STRUCTURE OF T.TH. HB8 CTP SYNTHETASE COMPLEX WITH GLUTAMINE

Authors :   M. Goto, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   10 Mar 04 (Deposition) - 31 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Tetramer, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Goto, R. Omi, N. Nakagawa, I. Miyahara, K. Hirotsu
Crystal Structures Of Ctp Synthetase Reveal Atp, Utp, And Glutamine Binding Sites
Structure V. 12 1413 2004
PubMed-ID: 15296735 | Reference-DOI: 10.1016/J.STR.2004.05.013
(for further references see the PDB file header)

Molecule 1 - CTP SYNTHETASE
	Chains	:	A
	EC Number	:	6.3.4.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	HB8
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GLN	1	Mod. Amino Acid	GLUTAMINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	GLN	4	Mod. Amino Acid	GLUTAMINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:64 , GLY A:363 , GLY A:364 , PHE A:365 , CYS A:391 , LEU A:392 , GLN A:395 , GLU A:415 , HIS A:471 , ARG A:472 , TYR A:473 , HOH A:753	BINDING SITE FOR RESIDUE GLN A 610

(no "SS Bond" information available for 1VCO)

Asymmetric Unit

No.	Residues
1	Ile A:125	-	Pro A:126

(no "SAP(SNP)/Variant" information available for 1VCO)

(no "PROSITE Motif" information available for 1VCO)

(no "Exon" information available for 1VCO)

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:532
 aligned with PYRG_THET8 | Q5SIA8 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:541
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549 
           PYRG_THET8    10 RPRKYVFITGGVVSSLGKGILTSSLGALLRARGYRVTAIKIDPYVNVDAGTMRPYEHGEVFVTADGAETDLDIGHYERFLDMDLSRGNNLTTGQVYLSVIQKERRGEYLSQTVQVIPHITDEIKERIRKVAEEQKAEIVVVEVGGTVGDIESLPFLEAIRQFRFDEGEGNTLYLHLTLVPYLETSEEFKTKPTQHSVATLRGVGIQPDILVLRSARPVPEEVRRKVALFTNVRPGHVFSSPTVEHLYEVPLLLEEQGLGRAVERALGLEAVIPNLSFWQEAVRVLKHPERTVKIAIAGKYVKMPDAYLSLLEALRHAGIKNRARVEVKWVDAESLEAADLDEAFRDVSGILVPGGFGVRGIEGKVRAAQYARERKIPYLGICLGLQIAVIEFARNVAGLKGANSTEFDPHTPHPVIDLMPEQLEVEGLGGTMRLGDWPMRIKPGTLLHRLYGKEEVLERHRHRYEVNPLYVDGLERAGLVVSATTPGMRGRGAGLVEAIELKDHPFFLGLQSHPEFKSRPMRPSPPFVGFVEAALAYQERA 550
               SCOP domains -d1vcoa2 A:11-282 CTP synthase PyrG, N-terminal domain                                                                                                                                                                                                                           ---------------d1vcoa1 A:298   -547 CTP synthase PyrG, C-termi  nal domain                                                                                                                                                                                               - - SCOP domains
               CATH domains 1vcoA01 A:10-296 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                          1vcoA02 A:297-   548  [code=3.40.50.880, no name   defined]                                                                                                                                                                                                  - CATH domains
               Pfam domains --CTP_synth_N-1vcoA02 A:12-287                                                                                                                                                                                                                                                        -----------------------   GATase-1vcoA01 A:314-542                                                                                                                                                                                                             ------ - Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhh....eeeeeee.....hhhhh........ee.....ee.hhhhhhhhhhh...hhh.eeehhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh...eeeeeeee..ee....ee.hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhh.hhh.eeeee.....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..eeeeeeeee...---..hhhhhhhhhhhhhhh.eeeeeeeee.hhh--.hhhhhh.....eee.......hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......ee.........eeeee.hhhhh.---....eeeeeeeee...hhhhhhhh..eeeeeeee.eeehhhhhhhhhhhheeeeee...........eeeeee.....eeee..hhhhhh.....hhhhhhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vco A  10 RPRKYVFITGGVVSSLGKGILTSSLGALLRARGYRVTAIKIDPYVNVDAGTMRPYEHGEVFVTADGAETDLDIGHYERFLDMDLSRGNNLTTGQVYLSVIQKERRGEYLSQTVQVIPHITDEIKERIRKVAEEQKAEIVVVEVGGTVGDIESLPFLEAIRQFRFDEGEGNTLYLHLTLVPYLETSEEFKTKPTQHSVATLRGVGIQPDILVLRSARPVPEEVRRKVALFTNVRPGHVFSSPTVEHLYEVPLLLEEQGLGRAVERALGLEAVIPNLSFWQEAVRVLKHPERTVKIAIAGKYV---DAYLSLLEALRHAGIKNRARVEVKWVDAESL--ADLEEAFRDVSGILVPGGFGVRGIEGKVRAAQYARERKIPYLGICLGLQIAVIEFARNVAGLKGANSTEFDPHTPHPVIDLMPEQLEV---GGTMRLGDWPMRIKPGTLLHRLYGKEEVLERHRHRYEVNPLYVDGLERAGLVVSATTPGMRGRGAGLVEAIELKDHPFFLGLQSHPEFKSRPMRPSPPFVGFVEAALAYQE-Q 610
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309|   |  319       329       339    |  349       359       369       379       389       399       409       419       429    |  439       449       459       469       479       489       499       509       519       529       539        |-|
                                                                                                                                                                                                                                                                                                                                      310 314                           344  |                                                                                    434 438                                                                                                           548 |
                                                                                                                                                                                                                                                                                                                                                                           347                                                                                                                                                                                                        610

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.880, no name defined] (97)

Thermus thermophilus. Organism_taxid: 274. (4)

1vcoA02

A:297-548

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Thermus thermophilus. Organism_taxid: 274. (12)

1vcoA01

A:10-296

Asymmetric Unit(hide GO term definitions)

Chain A (PYRG_THET8 | Q5SIA8)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003883	CTP synthase activity	Catalysis of the reaction: ATP + UTP + NH3 = ADP + phosphate + CTP.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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.
biological process
	GO:0044210	'de novo' CTP biosynthetic process	The chemical reactions and pathways resulting in the formation of cytidine 5'-triphosphate (CTP) from simpler components.
	GO:0006541	glutamine metabolic process	The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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	Cis Peptide Bonds
		Ile A:125 - Pro A:126	[ RasMol ]

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UniProtKB/Swiss-Prot
	PYRG_THET8 \| Q5SIA8	:	1vcm 1vcn

1vcm	NATIVE T.TH. HB8 CTP SYNTHETASE
1vcn	T.TH. HB8 CTP SYNTHETASE COMPLEX WITH SULFATE ANION RELATED ID: TTK003000122.3 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 2)

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