4U0M - JenaLib

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Title :   STRUCTURE OF THE VIBRIO CHOLERAE DI-NUCLEOTIDE CYCLASE (DNCV) MUTANT D193N IN COMPLEX WITH ATP, GTP AND 5MTHFGLU2

Authors :   D. Zhu, Y. Xiang

Date :   12 Jul 14 (Deposition) - 17 Sep 14 (Release) - 22 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Regulation, Mutation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Zhu, L. Wang, G. Shang, X. Liu, J. Zhu, D. Lu, L. Wang, B. Kan, J. R. Zhang, Y. Xiang
Structural Biochemistry Of A Vibrio Cholerae Dinucleotide Cyclase Reveals Cyclase Activity Regulation By Folates.
Mol. Cell V. 55 931 2014
PubMed-ID: 25201413 | Reference-DOI: 10.1016/J.MOLCEL.2014.08.001

Molecule 1 - CYCLIC AMP-GMP SYNTHASE
	Chains	:	A, B
	EC Number	:	2.7.7.86
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-419
	Gene	:	DNCV, VC_0179
	Mutation	:	YES
	Organism Scientific	:	VIBRIO CHOLERAE EL TOR N16961
	Organism Taxid	:	243277
	Synonym	:	C-AMP-GMP SYNTHASE,DINUCLEOTIDE CYCLASE DNCV

		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 (4, 7)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GTP	2	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	TLL	1	Ligand/Ion	N-[4-({[(6S)-2-AMINO-5-METHYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GAMMA-GLUTAMYL-L-GLUTAMIC ACID

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TLL	1	Ligand/Ion	N-[4-({[(6S)-2-AMINO-5-METHYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GAMMA-GLUTAMYL-L-GLUTAMIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TLL	-1	Ligand/Ion	N-[4-({[(6S)-2-AMINO-5-METHYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GAMMA-GLUTAMYL-L-GLUTAMIC ACID

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:112 , GLY A:113 , SER A:114 , TYR A:117 , ASP A:131 , ASP A:133 , VAL A:264 , LYS A:287 , SER A:301 , ASP A:348 , LEU A:352 , ATP A:502 , MG A:503 , HOH A:656 , HOH A:681 , HOH A:685 , HOH A:689 , HOH A:692 , HOH A:699 , HOH A:720 , HOH A:763 , HOH A:774	binding site for residue GTP A 501
2	AC2	SOFTWARE	GLN A:112 , ASP A:133 , LYS A:177 , THR A:179 , ARG A:182 , ASN A:193 , LEU A:247 , SER A:259 , GTP A:501	binding site for residue ATP A 502
3	AC3	SOFTWARE	ASP A:131 , ASP A:133 , GTP A:501 , HOH A:763	binding site for residue MG A 503
4	AC4	SOFTWARE	ARG A:36 , ARG A:40 , ARG A:44 , ARG A:108 , PHE A:109 , TRP A:110 , THR A:111 , GLN A:116 , TYR A:137 , PHE A:204 , GLN A:208 , GLU A:239 , LEU A:240 , ASP A:260 , PRO A:261 , LYS A:262 , HOH A:760 , HOH A:787	binding site for residue TLL A 504
5	AC5	SOFTWARE	GLN B:112 , GLY B:113 , SER B:114 , TYR B:117 , ASP B:131 , ASP B:133 , VAL B:264 , LYS B:287 , SER B:301 , ASP B:345 , ASP B:348 , LEU B:352 , ATP B:502 , MG B:503 , HOH B:649 , HOH B:668 , HOH B:678 , HOH B:685 , HOH B:708 , HOH B:724 , HOH B:730 , HOH B:739 , HOH B:765 , HOH B:766 , HOH B:778	binding site for residue GTP B 501
6	AC6	SOFTWARE	ASP B:131 , ASP B:133 , LYS B:177 , THR B:179 , ARG B:182 , HIS B:191 , ASN B:193 , SER B:259 , GTP B:501 , HOH B:695 , HOH B:702 , HOH B:708 , HOH B:739 , HOH B:762 , HOH B:776	binding site for residue ATP B 502
7	AC7	SOFTWARE	ASP B:131 , ASP B:133 , GTP B:501 , HOH B:724	binding site for residue MG B 503

(no "SS Bond" information available for 4U0M)

(no "Cis Peptide Bond" information available for 4U0M)

(no "SAP(SNP)/Variant" information available for 4U0M)

(no "PROSITE Motif" information available for 4U0M)

(no "Exon" information available for 4U0M)

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:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...eeeee.................eeeeeeeeeee.........hhhhhhhhhhhhhhhhhh....eeeee....eeeee....eeeee.eeeeehhhhhhhhhhhhhhh...hhhh.eee.......eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0m A   3 MTWNFHQYYTNRNDGLMGKLVLTDEEKNNLKALRKIIRLRTRDVFEEAKGIAKAVKKSALTFEIIQEKVSTTQIKHLSDSEQREVAKLIYEMDDDARDEFLGLTPRFWTQGSFQYDTLNRPFQPGQEMDIDDGTYMPMPIFESEPKIGHSLLILLVDASLKSLVAENHGWKFEAKQTCGRIKIEAEKTHINVPMYAIPKDEFQKKQIALEANRYELDSENVNLALREGDRKWINSDPKIVEDWFNDSCIRIGKHLRKVCRFMKAWRDAQWDVGGPSSISLMAATVNILDSVAHDASDLGETMKIIAKHLPSEFARGVESPDSTDEKPLFPPSYKHGPREMDIMSKLERLPEILSSAESADSKSEALKKINMAFGNRVTNSELIVLAK 411
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  ||   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       
                                                                                                                                                                                                                                              215|                                                                                                                                                                             
                                                                                                                                                                                                                                               238

Chain B from PDB  Type:PROTEIN  Length:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.................eeeeeeeeeee.........hhhhhhhhhhhhhhhhhh....eeeee....eeeee....eeeee.eeeeehhhhhhhhh...............eee.......eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0m B   3 MTWNFHQYYTNRNDGLMGKLVLTDEEKNNLKALRKIIRLRTRDVFEEAKGIAKAVKKSALTFEIIQEKVSTTQIKHLSDSEQREVAKLIYEMDDDARDEFLGLTPRFWTQGSFQYDTLNRPFQPGQEMDIDDGTYMPMPIFESEPKIGHSLLILLVDASLKSLVAENHGWKFEAKQTCGRIKIEAEKTHINVPMYAIPKDEFQKKQIALEANRTYELDSENVNLALREGDRKWINSDPKIVEDWFNDSCIRIGKHLRKVCRFMKAWRDAQWDVGGPSSISLMAATVNILDSVAHDASDLGETMKIIAKHLPSEFARGVESPDSTDEKPLFPPSYKHGPREMDIMSKLERLPEILSSAESADSKSEALKKINMAFGNRVTNSELIVLAK 411
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  ||   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403        
                                                                                                                                                                                                                                              215|                                                                                                                                                                              
                                                                                                                                                                                                                                               237

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 4U0M)

(no "CATH Domain" information available for 4U0M)

(no "Pfam Domain" information available for 4U0M)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4u0m)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4u0m
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	DNCV_VIBCH \| Q9KVG7
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	2.7.7.86
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	DNCV_VIBCH \| Q9KVG7	:	4txy 4txz 4ty0 4u03 4u0l 4u0n 4xj1 4xj3 4xj4 4xj5 5go3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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