1WZU - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF QUINOLINATE SYNTHASE (NADA)

Authors :   H. Sakuraba

Date :   09 Mar 05 (Deposition) - 07 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Nad, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Sakuraba, H. Tsuge, K. Yoneda, N. Katunuma, T. Ohshima
Crystal Structure Of The Nad Biosynthetic Enzyme Quinolinate Synthase
J. Biol. Chem. V. 280 26645 2005
PubMed-ID: 15937336 | Reference-DOI: 10.1074/JBC.C500192200
(for further references see the PDB file header)

Molecule 1 - QUINOLINATE SYNTHETASE A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953
	Synonym	:	NAD SYNTHESIS RELATED PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MLT	1	Ligand/Ion	MALATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:21 , ASP A:37 , SER A:38 , TYR A:109 , THR A:125 , SER A:126 , HIS A:196 , SER A:212 , THR A:213 , HOH A:302	BINDING SITE FOR RESIDUE MLT A 301

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:144	-	Pro A:145

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

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

(no "Exon" information available for 1WZU)

Asymmetric/Biological 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:271
 aligned with NADA_PYRHO | O57767 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        
           NADA_PYRHO     1 MDLVEEILRLKEERNAIILAHNYQLPEVQDIADFIGDSLELARRATRVDADVIVFAGVDFMAETAKILNPDKVVLIPSREATCAMANMLKVEHILEAKRKYPNAPVVLYVNSTAEAKAYADVTVTSANAVEVVKKLDSDVVIFGPDKNLAHYVAKMTGKKIIPVPSKGHCYVHQKFTLDDVERAKKLHPNAKLMIHPECIPEVQEKADIIASTGGMIKRACEWDEWVVFTEREMVYRLRKLYPQKKFYPAREDAFCIGMKAITLKNIYESLKDMKYKVEVPEEIARKARKAIERMLEM 298
               SCOP domains d1wzua1 A:1-298 Quinolinate synthetase A, NadA                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---NadA-1wzuA01 A:4-298                                                                                                                                                                                                                                                                                    Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeeee...hhhhhhhh.eeehhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eee...------------hhhhhhhhhhh....eeee...hhhhhh...eee...hhhhhhhh....eeeee.hhhhhhhhhhhhh.eeee.-----------.hhhhhhhhhhhh...eeee....hhhhhhh..ee.hhhhhhhhhhhh.eeeee..hhhhhhhhhhh...eeee.......----..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wzu A   1 MDLVEEILRLKEERNAIILAHNYQLPEVQDIADFIGDSLELARRATRVDADVIVFAGVDFMAETAKILNPDKVVLIPS------------VEHILEAKRKYPNAPVVLYVNSTAEAKAYADVTVTSANAVEVVKKLDSDVVIFGPDKNLAHYVAKMTGKKIIPV-----------FTLDDVERAKKLHPNAKLMIHPECIPEVQEKADIIASTGGMIKRACEWDEWVVFTEREMVYRLRKLYPQKKFYPAREDAFC----AITLKNIYESLKDMKYKVEVPEEIARKARKAIERMLEM 298
                                    10        20        30        40        50        60        70       | -         -|      100       110       120       130       140       150       160   |     -     | 180       190       200       210       220       230       240       250     |   -|      270       280       290        
                                                                                                        78           91                                                                      164         176                                                                             256  261

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NadA-like (2)

Superfamily: NadA-like (2)

Family: NadA-like (1)

Protein domain: Quinolinate synthetase A, NadA (1)

Pyrococcus horikoshii [TaxId: 53953] (1)

d1wzua1

A:1-298

(no "CATH Domain" information available for 1WZU)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: NadA] (1)

Family: NadA (1)

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (1)

NadA-1wzuA01

A:4-298

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NADA_PYRHO | O57767)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008987	quinolinate synthetase A activity	Catalysis of the reaction: iminoaspartate + dihydroxy-acetone-phosphate = quinolinate + 2 H2O + phosphate.
	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.
	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
	GO:0009435	NAD biosynthetic process	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
	GO:0019363	pyridine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.
	GO:0019805	quinolinate biosynthetic process	The chemical reactions and pathways resulting in the formation of quinolinate, the anion of quinolinic acid, also known as 2,3-pyridinedicarboxylic acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MLT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:144 - Pro A:145	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1wzu
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NADA_PYRHO \| O57767
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	NADA_PYRHO \| O57767
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NADA_PYRHO \| O57767	:	4zk6 5ktm 5ktn 5kto 5ktp 5ktr 5kts 5ktt

(no "Related Entries Specified in the PDB File" available for 1WZU)

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)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File