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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE ANALYSIS OF HUMAN SERINE DEHYDRATASE

Authors :   L. Sun, Y. Liu, Z. Rao

Date :   27 Apr 03 (Deposition) - 01 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Sun, X. Li, Y. Dong, M. Yang, Y. Liu, X. Han, X. Zhang, H. Pang, Z. Rao
Crystallization And Preliminary Crystallographic Analysis O Human Serine Dehydratase.
Acta Crystallogr. , Sect. D V. 59 2297 2003
PubMed-ID: 14646100 | Reference-DOI: 10.1107/S0907444903020110

Molecule 1 - L-SERINE DEHYDRATASE
	Chains	:	A
	EC Number	:	4.3.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organ	:	LIVER
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SERINE DEHYDRATASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:40 , LYS A:41 , ASN A:67 , SER A:166 , VAL A:167 , GLY A:168 , GLY A:169 , GLY A:170 , GLY A:171 , LEU A:172 , ALA A:269 , CYS A:303 , GLY A:304 , GLY A:305 , HOH A:418 , HOH A:420	BINDING SITE FOR RESIDUE PLP A 941

(no "SS Bond" information available for 1P5J)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:293	-	Pro A:294

(no "SAP(SNP)/Variant" information available for 1P5J)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDRATASE_SER_THR	PS00165	Serine/threonine dehydratases pyridoxal-phosphate attachment site.	SDHL_HUMAN	32-45	1	A:32-45

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000257549	1	ENSE00001342492	chr12:113841688-113841573	116	SDHL_HUMAN	-	0	0	-	-
1.2	ENST00000257549	2	ENSE00000998111	chr12:113837515-113837361	155	SDHL_HUMAN	1-51	51	1	A:4-51	48
1.3	ENST00000257549	3	ENSE00000918014	chr12:113836956-113836917	40	SDHL_HUMAN	52-65	14	1	A:52-65	14
1.4	ENST00000257549	4	ENSE00000918013	chr12:113836651-113836512	140	SDHL_HUMAN	65-111	47	1	A:65-111	47
1.5	ENST00000257549	5	ENSE00000918012	chr12:113836411-113836320	92	SDHL_HUMAN	112-142	31	1	A:112-142	31
1.6	ENST00000257549	6	ENSE00000918011	chr12:113835197-113834970	228	SDHL_HUMAN	142-218	77	1	A:142-218	77
1.7	ENST00000257549	7	ENSE00000918010	chr12:113831821-113831697	125	SDHL_HUMAN	218-260	43	1	A:218-260	43
1.8	ENST00000257549	8	ENSE00000918009	chr12:113830954-113830253	702	SDHL_HUMAN	260-328	69	1	A:260-322	63

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:319
 aligned with SDHL_HUMAN | P20132 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:319
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313         
           SDHL_HUMAN     4 GEPLHVKTPIRDSMALSKMAGTSVYLKMDSAQPSGSFKIRGIGHFCKRWAKQGCAHFVCSSAGNAGMAAAYAARQLGVPATIVVPSTTPALTIERLKNEGATVKVVGELLDEAFELAKALAKNNPGWVYIPPFDDPLIWEGHASIVKELKETLWEKPGAIALSVGGGGLLCGVVQGLQEVGWGDVPVIAMETFGAHSFHAATTAGKLVSLPKITSVAKALGVKTVGAQALKLFQEHPIFSEVISDQEAVAAIEKFVDDEKILVEPACGAALAAVYSHVIQKLQLEGNLRTPLPSLVVIVCGGSNISLAQLRALKEQLGM 322
               SCOP domains d1p5ja_ A: L-serine dehydratase                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1p5jA01 A:4-40,A:137-322             1p5jA02 A:41-136  [code=3.40.50.1100, no name defined]                                          1p5jA01 A:4-40,A:137-322  [code=3.40.50.1100, no name defined]                                                                                                                             CATH domains
               Pfam domains -PALP-1p5jA01 A:5-304                                                                                                                                                                                                                                                                                        ------------------ Pfam domains
         Sec.struct. author .........eeeehhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh......eeeeee...hhhhhhhhhh...........hhhhh....hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.........eeee.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------DEHYDRATASE_SE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:4-51 UniProt: 1-51 [INCOMPLETE]Exon 1.3      ----------------------------------------------Exon 1.5  PDB: A:112-142       ---------------------------------------------------------------------------Exon 1.7  PDB: A:218-260 UniProt: 218-260  -------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.4  PDB: A:65-111 UniProt: 65-111        ------------------------------Exon 1.6  PDB: A:142-218 UniProt: 142-218                                    -----------------------------------------Exon 1.8  PDB: A:260-322 UniProt: 260-328 [INCOMPLETE]          Transcript 1 (2)
                 1p5j A   4 GEPLHVKTPIRDSMALSKMAGTSVYLKMDSAQPSGSFKIRGIGHFCKRWAKQGCAHFVCSSAGNAGMAAAYAARQLGVPATIVVPGTTPALTIERLKNEGATCKVVGELLDEAFELAKALAKNNPGWVYIPPFDDPLIWEGHASIVKELKETLWEKPGAIALSVGGGGLLCGVVQGLQECGWGDVPVIAMETFGAHSFHAATTAGKLVSLPKITSVAKALGVKTVGSQALKLFQEHPIFSEVISDQEAVAAIEKFVDDEKILVEPACGAALAAVYSHVIQKLQLEGNLRTPLPSLVVIVCGGSNISLAQLRALKEQLGM 322
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1100, no name defined] (77)

Human (Homo sapiens) (4)

1a	1p5jA01	A:4-40,A:137-322
1b	1p5jA02	A:41-136

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PALP] (67)

Family: PALP (67)

Homo sapiens (Human) (6)

PALP-1p5jA01

A:5-304

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SDHL_HUMAN | P20132)

molecular function
	GO:0003941	L-serine ammonia-lyase activity	Catalysis of the reaction: L-serine = pyruvate + NH3.
	GO:0004794	L-threonine ammonia-lyase activity	Catalysis of the reaction: L-threonine = 2-oxobutanoate + NH3.
	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.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
	GO:0006565	L-serine catabolic process	The chemical reactions and pathways resulting in the breakdown of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0042866	pyruvate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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/Biological Unit
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		Thr A:293 - Pro A:294	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1P5J)

Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (7, 7)

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