3S5N - JenaLib

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

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 :   2.50

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

Keywords :   Aldolase, Beta Barrel, 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

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:187 , HIS A:189 , ILE A:192 , ASP A:216 , HOH A:353 , HOH A:370	BINDING SITE FOR RESIDUE K A 330
2	AC2	SOFTWARE	THR A:212 , GLN A:215 , PHE A:217 , HOH A:383 , HOH A:384	BINDING SITE FOR RESIDUE NA A 331
3	AC3	SOFTWARE	EDO A:2 , LYS A:63 , PHE A:295 , GLY A:296 , TYR A:297 , HOH A:381	BINDING SITE FOR RESIDUE EDO A 1
4	AC4	SOFTWARE	EDO A:1 , LYS A:63 , HOH A:380	BINDING SITE FOR RESIDUE EDO A 2
5	AC5	SOFTWARE	VAL A:42 , THR A:43 , PRO A:45 , ASN A:60 , ASN A:244 , MET A:292	BINDING SITE FOR RESIDUE EDO A 3
6	AC6	SOFTWARE	EDO A:6 , GLY A:143 , ARG A:144 , THR A:280 , ARG A:281 , ARG A:282 , GLY A:284	BINDING SITE FOR RESIDUE EDO A 4
7	AC7	SOFTWARE	EDO A:6 , SER A:77 , TYR A:141 , ASN A:173 , THR A:280 , HOH A:385 , HOH A:386	BINDING SITE FOR RESIDUE EDO A 5
8	AC8	SOFTWARE	EDO A:4 , EDO A:5 , TYR A:141 , GLY A:143 , ARG A:144 , GLY A:284 , ILE A:285 , PRO A:286 , LEU A:306	BINDING SITE FOR RESIDUE EDO A 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

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:295
 aligned with HOGA1_HUMAN | Q86XE5 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:295
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322     
          HOGA1_HUMAN    33 VDIAGIYPPVTTPFTATAEVDYGKLEENLHKLGTFPFRGFVVQGSNGEFPFLTSSERLEVVSRVRQAMPKNRLLLAGSGCESTQATVEMTVSMAQVGADAAMVVTPCYYRGRMSSAALIHHYTKVADLSPIPVVLYSVPANTGLDLPVDAVVTLSQHPNIVGMKDSGGDVTRIGLIVHKTRKQDFQVLAGSAGFLMASYALGAVGGVCALANVLGAQVCQLERLCCTGQWEDAQKLQHRLIEPNAAVTRRFGIPGLKKIMDWFGYYGGPCRAPLQELSPAEEEALRMDFTSNGWL 327
               SCOP domains d3s5na_ A: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.ee..........hhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeee.hhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..............hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G-----------------------------V---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: A:168-198        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s5n A  33 VDIAGIYPPVTTPFTATAEVDYGKLEENLHKLGTFPFRGFVVQGSNGEFPFLTSSERLEVVSRVRQAMPKNRLLLAGSGCESTQATVEMTVSMAQVGADAAMVVTPCYYRGRMSSAALIHHYTKVADLSPIPVVLYSVPANTGLDLPVDAVVTLSQHPNIVGMKDSGGDVTRIGLIVHKTRKQDFQVLAGSAGFLMASYALGAVGGVCALANVLGAQVCQLERLCCTGQWEDAQKLQHRLIEPNAAVTRRFGIPGLKKIMDWFGYYGGPCRAPLQELSPAEEEALRMDFTSNGWL 327
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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.

Visualization

Interactive Views

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 ]
		NA	[ 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 ]

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

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3s5n
		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

Description