4U03 - JenaLib

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

Authors :   D. Y. Zhu, Y. Xiang

Date :   11 Jul 14 (Deposition) - 17 Sep 14 (Release) - 22 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

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

Keywords :   Regulation, 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 BL21(DE3)
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-419
	Gene	:	DNCV, VC_0179
	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 (3, 10)

No.	Name	Count	Type	Full Name
1	GTP	4	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	TLL	2	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 (2, 3)

No.	Name	Count	Type	Full Name
1	GTP	2	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	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, 3)

No.	Name	Count	Type	Full Name
1	GTP	2	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	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 (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:112 , GLY A:113 , SER A:114 , TYR A:117 , ASP A:131 , ASP A:133 , LYS A:287 , SER A:301 , ASP A:345 , ASP A:348 , LEU A:352 , GTP A:502 , MG A:503 , HOH A:643 , HOH A:658 , HOH A:663 , HOH A:665 , HOH A:680 , HOH A:691 , HOH A:742 , HOH A:748 , HOH A:757	binding site for residue GTP A 501
02	AC2	SOFTWARE	GLN A:112 , ASP A:131 , ASP A:133 , LYS A:177 , THR A:179 , CYS A:180 , ARG A:182 , ASP A:193 , TYR A:197 , LEU A:247 , SER A:259 , GTP A:501 , MG A:504 , HOH A:757	binding site for residue GTP A 502
03	AC3	SOFTWARE	ASP A:131 , ASP A:133 , GTP A:501 , HOH A:750	binding site for residue MG A 503
04	AC4	SOFTWARE	ASP A:131 , ASP A:133 , ASP A:193 , GTP A:502 , HOH A:757	binding site for residue MG A 504
05	AC5	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 , TYR A:238 , GLU A:239 , LEU A:240 , ASP A:260 , PRO A:261 , LYS A:262	binding site for residue TLL A 505
06	AC6	SOFTWARE	GLN B:112 , GLY B:113 , SER B:114 , TYR B:117 , ASP B:131 , ASP B:133 , LYS B:287 , ARG B:290 , SER B:301 , ASP B:345 , ASP B:348 , LEU B:352 , GTP B:502 , MG B:503 , HOH B:630 , HOH B:633 , HOH B:688 , HOH B:689 , HOH B:691 , HOH B:692 , HOH B:700 , HOH B:706 , HOH B:714	binding site for residue GTP B 501
07	AC7	SOFTWARE	GLN B:112 , ASP B:133 , LYS B:177 , THR B:179 , CYS B:180 , ARG B:182 , ASP B:193 , TYR B:197 , SER B:259 , GTP B:501 , MG B:504 , HOH B:653 , HOH B:665 , HOH B:714	binding site for residue GTP B 502
08	AC8	SOFTWARE	ASP B:131 , ASP B:133 , GTP B:501 , HOH B:710	binding site for residue MG B 503
09	AC9	SOFTWARE	ASP B:131 , ASP B:133 , ASP B:193 , GTP B:502 , HOH B:714	binding site for residue MG B 504
10	AD1	SOFTWARE	ARG B:36 , ARG B:40 , ARG B:108 , PHE B:109 , TRP B:110 , THR B:111 , GLN B:116 , TYR B:137 , PHE B:204 , TYR B:238 , GLU B:239 , LEU B:240 , SER B:242 , ASP B:260 , PRO B:261 , LYS B:262	binding site for residue TLL B 505

(no "SS Bond" information available for 4U03)

(no "Cis Peptide Bond" information available for 4U03)

(no "SAP(SNP)/Variant" information available for 4U03)

(no "PROSITE Motif" information available for 4U03)

(no "Exon" information available for 4U03)

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:389
                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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.eeeeehhhhhhhhhhhhhh......hhhh.eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u03 A   3 MTWNFHQYYTNRNDGLMGKLVLTDEEKNNLKALRKIIRLRTRDVFEEAKGIAKAVKKSALTFEIIQEKVSTTQIKHLSDSEQREVAKLIYEMDDDARDEFLGLTPRFWTQGSFQYDTLNRPFQPGQEMDIDDGTYMPMPIFESEPKIGHSLLILLVDASLKSLVAENHGWKFEAKQTCGRIKIEAEKTHIDVPMYAIPKDEFQKKQIALEANRSFYELDSENVNLALREGDRKWINSDPKIVEDWFNDSCIRIGKHLRKVCRFMKAWRDAQWDVGGPSSISLMAATVNILDSVAHDASDLGETMKIIAKHLPSEFARGVESPDSTDEKPLFPPSYKHGPREMDIMSKLERLPEILSSAESADSKSEALKKINMAFGNRVTNSELIVLAK 411
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    || 242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402         
                                                                                                                                                                                                                                                217|                                                                                                                                                                             
                                                                                                                                                                                                                                                 238

Chain B from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.................eeeeeeeeeee.........hhhhhhhhhhhhhhhhhh....eeeee....eeeee....eeeee.eeeeehhhhhhhhhh.....hhhh.eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u03 B   2 RMTWNFHQYYTNRNDGLMGKLVLTDEEKNNLKALRKIIRLRTRDVFEEAKGIAKAVKKSALTFEIIQEKVSTTQIKHLSDSEQREVAKLIYEMDDDARDEFLGLTPRFWTQGSFQYDTLNRPFQPGQEMDIDDGTYMPMPIFESEPKIGHSLLILLVDASLKSLVAENHGWKFEAKQTCGRIKIEAEKTHIDVPMYAIPKDEFQKKQIALTYELDSENVNLALREGDRKWINSDPKIVEDWFNDSCIRIGKHLRKVCRFMKAWRDAQWDVGGPSSISLMAATVNILDSVAHDASDLGETMKIIAKHLPSEFARGVESPDSTDEKPLFPPSYKHGPREMDIMSKLERLPEILSSAESADSKSEALKKINMAFGNRVTNSELIVLAK 411
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211|      246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406     
                                                                                                                                                                                                                                           211|                                                                                                                                                                              
                                                                                                                                                                                                                                            237

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 4U03)

(no "CATH Domain" information available for 4U03)

(no "Pfam Domain" information available for 4U03)

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	Cis Peptide Bonds
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	4u03
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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 4u0l 4u0m 4u0n 4xj1 4xj3 4xj4 4xj5 5go3

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Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

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