3S5O - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN 4-HYDROXY-2-OXOGLUTARATE ALDOLASE BOUND TO PYRUVATE

Authors :   T. J. Riedel, W. T. Lowther

Date :   23 May 11 (Deposition) - 26 Oct 11 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.97

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

Keywords :   Aldolase, Beta Barrel, Schiff Base, Hydroxyproline Metabolism, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. J. Riedel, L. C. Johnson, J. Knight, R. R. Hantgan, R. P. Holmes, W. T. Lowther
Structural And Biochemical Studies Of Human 4-Hydroxy-2-Oxoglutarate Aldolase: Implications For Hydroxyproline Metabolism In Primary Hyperoxaluria.
Plos One V. 6 26021 2011
PubMed-ID: 21998747 | Reference-DOI: 10.1371/JOURNAL.PONE.0026021

Molecule 1 - 4-HYDROXY-2-OXOGLUTARATE ALDOLASE, MITOCHONDRIAL
	Chains	:	A
	EC Number	:	4.1.3.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMAL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	C10ORF65, DHDPSL, HOGA1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DIHYDRODIPICOLINATE SYNTHASE-LIKE, DHDPS-LIKE PROTEIN, 2- KETO-4-HYDROXYGLUTARATE ALDOLASE, KHG-ALDOLASE, PROTEIN 569272

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	K	1	Ligand/Ion	POTASSIUM ION
3	KPI	1	Mod. Amino Acid	(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID

Biological Unit 1 (2, 28)

No.	Name	Count	Type	Full Name
1	EDO	24	Ligand/Ion	1,2-ETHANEDIOL
2	K	-1	Ligand/Ion	POTASSIUM ION
3	KPI	4	Mod. Amino Acid	(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:59 , LYS A:63 , HOH A:527 , HOH A:533	BINDING SITE FOR RESIDUE EDO A 1
2	AC2	SOFTWARE	LYS A:63 , PHE A:295 , GLY A:296 , TYR A:297 , HOH A:526 , HOH A:527	BINDING SITE FOR RESIDUE EDO A 2
3	AC3	SOFTWARE	EDO A:6 , TYR A:141 , ARG A:144 , GLY A:284 , ILE A:285 , PRO A:286 , HOH A:478 , HOH A:529	BINDING SITE FOR RESIDUE EDO A 3
4	AC4	SOFTWARE	VAL A:42 , THR A:43 , PRO A:45 , LEU A:57 , ASN A:60 , LEU A:64 , ASN A:244 , MET A:292	BINDING SITE FOR RESIDUE EDO A 4
5	AC5	SOFTWARE	EDO A:3 , SER A:77 , ASN A:173 , HOH A:341 , HOH A:537	BINDING SITE FOR RESIDUE EDO A 6
6	AC6	SOFTWARE	SER A:187 , HIS A:189 , ILE A:192 , ASP A:216 , HOH A:342 , HOH A:371	BINDING SITE FOR RESIDUE K A 328

(no "SS Bond" information available for 3S5O)

Asymmetric Unit

No.	Residues
1	Ala A:304	-	Pro A:305

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_064035	C	257	G	HOGA1_HUMAN	Disease (HP3)	267606764	A	C	257	G
2	UniProt	VAR_064036	G	287	V	HOGA1_HUMAN	Disease (HP3)	138207257	A	G	287	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_064035	C	257	G	HOGA1_HUMAN	Disease (HP3)	267606764	A	C	257	G
2	UniProt	VAR_064036	G	287	V	HOGA1_HUMAN	Disease (HP3)	138207257	A	G	287	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	HOGA1_HUMAN	168-198	1	A:168-198

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	HOGA1_HUMAN	168-198	4	A:168-198

(no "Exon" information available for 3S5O)

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:296
 aligned with HOGA1_HUMAN | Q86XE5 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:296
                                    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      
          HOGA1_HUMAN    32 KVDIAGIYPPVTTPFTATAEVDYGKLEENLHKLGTFPFRGFVVQGSNGEFPFLTSSERLEVVSRVRQAMPKNRLLLAGSGCESTQATVEMTVSMAQVGADAAMVVTPCYYRGRMSSAALIHHYTKVADLSPIPVVLYSVPANTGLDLPVDAVVTLSQHPNIVGMKDSGGDVTRIGLIVHKTRKQDFQVLAGSAGFLMASYALGAVGGVCALANVLGAQVCQLERLCCTGQWEDAQKLQHRLIEPNAAVTRRFGIPGLKKIMDWFGYYGGPCRAPLQELSPAEEEALRMDFTSNGWL 327
               SCOP domains d3s5oa_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.............hhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeee.hhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.............hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-----------------------------V---------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: A:168-198        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s5o A  32 KVDIAGIYPPVTTPFTATAEVDYGKLEENLHKLGTFPFRGFVVQGSNGEFPFLTSSERLEVVSRVRQAMPKNRLLLAGSGCESTQATVEMTVSMAQVGADAAMVVTPCYYRGRMSSAALIHHYTKVADLSPIPVVLYSVPANTGLDLPVDAVVTLSQHPNIVGMkDSGGDVTRIGLIVHKTRKQDFQVLAGSAGFLMASYALGAVGGVCALANVLGAQVCQLERLCCTGQWEDAQKLQHRLIEPNAAVTRRFGIPGLKKIMDWFGYYGGPCRAPLQELSPAEEEALRMDFTSNGWL 327
                                    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      
                                                                                                                                                                                              196-KPI

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: automated matches (113)

Protein domain: automated matches (113)

Human (Homo sapiens) [TaxId: 9606] (2)

d3s5oa_

(no "CATH Domain" information available for 3S5O)

(no "Pfam Domain" information available for 3S5O)

Asymmetric Unit(hide GO term definitions)

Chain A (HOGA1_HUMAN | Q86XE5)

molecular function
	GO:0008700	4-hydroxy-2-oxoglutarate aldolase activity	Catalysis of the reaction: 4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate.
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0019470	4-hydroxyproline catabolic process	The chemical reactions and pathways resulting in the breakdown of 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline.
	GO:0009436	glyoxylate catabolic process	The chemical reactions and pathways resulting in the breakdown of glyoxylate, the anion of glyoxylic acid, HOC-COOH.
	GO:0046487	glyoxylate metabolic process	The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0033609	oxalate metabolic process	The chemical reactions and pathways involving oxalate, the organic acid ethanedioate.
	GO:0042866	pyruvate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		KPI	[ 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 ]

	Cis Peptide Bonds
		Ala A:304 - Pro A:305	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	3s5o
		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
	HOGA1_HUMAN \| Q86XE5
		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)
	4.1.3.16
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	613616
		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
	HOGA1_HUMAN \| Q86XE5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	HOGA1_HUMAN \| Q86XE5	:	3s5n

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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