3PUG - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HALOFERAX VOLCANII MALATE SYNTHASE NATIVE AT 3MM GLYOXYLATE

Authors :   B. R. Howard, C. D. Bracken, A. M. Neighbor, G. C. Thomas, K. K. Lamlenn, H. L. Schubert, F. G. Whitby

Date :   04 Dec 10 (Deposition) - 01 Jun 11 (Release) - 01 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)
Biol. Unit 2: A  (6x)

Keywords :   Tim Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. D. Bracken, A. M. Neighbor, K. K. Lamlenn, G. C. Thomas, H. L. Schubert, F. G. Whitby, B. R. Howard
Crystal Structures Of A Halophilic Archaeal Malate Synthase From Haloferax Volcanii And Comparisons With Isoforms A And G.
Bmc Struct. Biol. V. 11 23 2011
PubMed-ID: 21569248 | Reference-DOI: 10.1186/1472-6807-11-23

Molecule 1 - MALATE SYNTHASE
	Chains	:	A
	EC Number	:	2.3.3.9
	Organism Scientific	:	HALOFERAX VOLCANII
	Organism Taxid	:	309800
	Other Details	:	ATCC
	Strain	:	ATCC 29605, DS2

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A
Biological Unit 2 (6x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	GLV	1	Ligand/Ion	GLYOXYLIC ACID
3	K	4	Ligand/Ion	POTASSIUM ION
4	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GLV	3	Ligand/Ion	GLYOXYLIC ACID
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GLV	6	Ligand/Ion	GLYOXYLIC ACID
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:84 , GLU A:158 , GLY A:189 , GLU A:190 , VAL A:191 , ASP A:192 , PRO A:231 , HOH A:476 , HOH A:485 , MG A:601	BINDING SITE FOR RESIDUE GLV A 501
02	AC2	SOFTWARE	ASP A:52 , GLU A:158 , ASP A:192 , HOH A:476 , GLV A:501 , K A:803	BINDING SITE FOR RESIDUE MG A 601
03	AC3	SOFTWARE	ARG A:198 , ALA A:227 , K A:802	BINDING SITE FOR RESIDUE CL A 701
04	AC4	SOFTWARE	ARG A:89 , PRO A:92 , ARG A:95	BINDING SITE FOR RESIDUE CL A 702
05	AC5	SOFTWARE	ALA A:208	BINDING SITE FOR RESIDUE CL A 703
06	AC6	SOFTWARE	ARG A:218	BINDING SITE FOR RESIDUE CL A 704
07	AC7	SOFTWARE	MET A:173 , LYS A:175 , ASN A:178 , GLU A:181 , HOH A:435	BINDING SITE FOR RESIDUE K A 801
08	AC8	SOFTWARE	MET A:197 , SER A:217 , SER A:221 , GLY A:252 , CL A:701	BINDING SITE FOR RESIDUE K A 802
09	AC9	SOFTWARE	GLU A:51 , ASP A:52 , GLU A:123 , ASP A:192 , HOH A:476 , MG A:601	BINDING SITE FOR RESIDUE K A 803
10	BC1	SOFTWARE	PRO A:176 , ASN A:178 , ASN A:179	BINDING SITE FOR RESIDUE K A 804

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

(no "Cis Peptide Bond" information available for 3PUG)

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

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

(no "Exon" information available for 3PUG)

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:349
 aligned with ACEB_HALVD | D4GTL2 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:431
                                    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       321       331       341       351       361       371       381       391       401       411       421       431 
           ACEB_HALVD     2 TERRHDREFVRTFFTSPTAVEGEDDSAKMLRRAAGLRGMQAPDVWVPDNEDATAPSMRDEGAENIVEVISEQGAEFPGEIHPRMVWHRDSPETRYQGFQHMLDITDPERGAVEHIHGFVIPEVGGIDDWKKADEFFTIVEHEHGLDEGSLAMSVIIESGEAELAMGDLRDEMGKPTNNLERLFLLVDGEVDYTKDMRAMTPTGELPAWPELRHNTSRGASAAGCVAVDGPYDDIRDVEGYRERMTDNQAKGMLGIWSLTPGQVVEANTSPLPPKTGSWLLDADGEEVELASEDGVEAYDGDRLSLEATDGGYELRVGGDARELTADELREELLGLTSYVPSMDDIVDSMEEFEAAKEAGRGAIAMTQSATLRIGGTEIDIEKDRMWDEATYQAAMTPISLFQDVYENRPDQHEELEERYGAGVVERAMEVG 432
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee....--...hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..ee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhh.hhhhhh.....hhh.eeeeeehhhhhhhhh...........hhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhh....eeee.hhhhhhhhhhh............------------------------------------------------.hhhhhh....hhhhhhhhhhhhh--------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pug A   2 TERRHDREFVRTFFTSPTAVE--DDSAKMLRRAAGLRGMQAPDVWVPDNEDATAPSMRDEGAENIVEVISEQGAEFPGEIHPRMVWHRDSPETRYQGFQHMLDITDPERGAVEHIHGFVIPEVGGIDDWKKADEFFTIVEHEHGLDEGSLAMSVIIESGEAELAMGDLRDEMGKPTNNLERLFLLVDGEVDYTKDMRAMTPTGELPAWPELRHNTSRGASAAGCVAVDGPYDDIRDVEGYRERMTDNQAKGMLGIWSLTPGQVVEANTSPLPPKTGSWLLD------------------------------------------------EELLGLTSYVPSMDDIVDSMEEFE--------------------------------WDEATYQAAMTPISLFQDVYENRPDQHEELEERYGAGVVERAMEVG 432
                                    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|        -         -         -         -       331       341       351  |      -         -         -     | 391       401       411       421       431 
                                               22 25                                                                                                                                                                                                                                                              282                                              331                    354                              387

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 3PUG)

(no "CATH Domain" information available for 3PUG)

(no "Pfam Domain" information available for 3PUG)

Asymmetric Unit(hide GO term definitions)

Chain A (ACEB_HALVD | D4GTL2)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004474	malate synthase activity	Catalysis of the reaction: acetyl-CoA + glyoxylate + H(2)O = (S)-malate + CoA + H(+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0006097	glyoxylate cycle	A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
	GO:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric 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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GLV	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pug)

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 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
	3pug
		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
	ACEB_HALVD \| D4GTL2
		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)
	2.3.3.9
		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
	ACEB_HALVD \| D4GTL2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ACEB_HALVD \| D4GTL2	:	3oyx 3oyz 5tao

3oyx	HIGH-OCCUPANCY GLYOXYLATE COMPLEX
3oyz	PYRUVATE/ACETYL-COA TERNARY COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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