1L8L - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   MOLECULAR BASIS FOR THE LOCAL CONFOMATIONAL REARRANGEMENT OF HUMAN PHOSPHOSERINE PHOSPHATASE

Authors :   H. Y. Kim, Y. S. Heo, J. H. Kim, M. H. Park, J. Moon, S. Y. Park, T. G. Lee, Y. H. Jeon, S. Ro, K. Y. Hwang

Date :   21 Mar 02 (Deposition) - 01 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.51

Chains :   Asym./Biol. Unit : A,B

Keywords :   Phosphatase, Conformational Rearrangement, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Y. Kim, Y. S. Heo, J. H. Kim, M. H. Park, J. Moon, E. Kim, D. Kwon, J. Yoon, D. Shin, E. J. Jeong, S. Y. Park, T. G. Lee, Y. H. Jeon, S. Ro, J. M. Cho, K. Y. Hwang
Molecular Basis For The Local Conformational Rearrangement Of Human Phosphoserine Phosphatase.
J. Biol. Chem. V. 277 46651 2002
PubMed-ID: 12213811 | Reference-DOI: 10.1074/JBC.M204866200
(for further references see the PDB file header)

Molecule 1 - L-3-PHOSPHOSERINE PHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PSP, O-PHOSPHOSERINE PHOSPHOHYDROLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	APO	2	Ligand/Ion	D-2-AMINO-3-PHOSPHONO-PROPIONIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , GLU A:29 , SER A:109 , GLY A:110 , LYS A:158 , ASP A:179 , GLY A:180 , THR A:182	BINDING SITE FOR RESIDUE APO A 800
2	AC2	SOFTWARE	ASP B:20 , VAL B:21 , ASP B:22 , SER B:109 , GLY B:110 , LYS B:158 , THR B:182 , ASP B:183 , ARG B:202	BINDING SITE FOR RESIDUE APO B 801

(no "SS Bond" information available for 1L8L)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:7	-	Arg A:8

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022378	D	32	N	SERB_HUMAN	Disease (PSPHD)	28933976	A/B	D	32	N
2	UniProt	VAR_022379	M	52	T	SERB_HUMAN	Disease (PSPHD)	104894036	A/B	M	52	T

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

(no "PROSITE Motif" information available for 1L8L)

Asymmetric/Biological Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000395471	1a	ENSE00001749046	chr7:56119297-56118831	467	SERB_HUMAN	-	0	0	-	-
1.3d	ENST00000395471	3d	ENSE00001638092	chr7:56101847-56101654	194	SERB_HUMAN	-	0	0	-	-
1.5a	ENST00000395471	5a	ENSE00001337387	chr7:56099747-56099622	126	SERB_HUMAN	-	0	0	-	-
1.6c	ENST00000395471	6c	ENSE00002171169	chr7:56088924-56088766	159	SERB_HUMAN	1-47	47	2	A:4-47 B:4-47	44 44
1.7b	ENST00000395471	7b	ENSE00001018705	chr7:56087427-56087293	135	SERB_HUMAN	47-92	46	2	A:47-92 B:47-92	46 46
1.8b	ENST00000395471	8b	ENSE00001121162	chr7:56085072-56084927	146	SERB_HUMAN	92-141	50	2	A:92-141 B:92-141	50 50
1.9b	ENST00000395471	9b	ENSE00000976989	chr7:56082864-56082716	149	SERB_HUMAN	141-190	50	2	A:141-190 B:141-190	50 50
1.10c	ENST00000395471	10c	ENSE00001521802	chr7:56079562-56078761	802	SERB_HUMAN	191-225	35	2	A:191-225 B:191-225	35 35

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:222
 aligned with SERB_HUMAN | P78330 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:222
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
           SERB_HUMAN     4 HSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE 225
               SCOP domains d1l8la_ A: Phosphoserine phosphatase                                                                                                                                                                                           SCOP domains
               CATH domains 1l8lA01                   1l8lA02 A:30-80,A:135-146                          1l8lA01 A:4-29,A:81-134,A:147-225                     1l8lA02     1l8lA01 A:4-29,A:81-134,A:147-225  [code=3.40.50.1000, no name defined]         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh.eeeee..........hhhhhhh..hhhhhh...........hhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhh...eeeeeeeeehhhhhhhhhhh......eeee.eeee....eeee...hhhhh..hhhhhhhhhhhhhh...eeeee.hhhhhh......eeeee.....hhhhhh....ee......hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------N-------------------T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6c  PDB: A:4-47 UniProt: 1-47        --------------------------------------------Exon 1.8b  PDB: A:92-141 UniProt: 92-141          -------------------------------------------------Exon 1.10c  PDB: A:191-225          Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.7b  PDB: A:47-92 UniProt: 47-92        ------------------------------------------------Exon 1.9b  PDB: A:141-190 UniProt: 141-190        ----------------------------------- Transcript 1 (2)
                 1l8l A   4 HSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKFLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE 225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with SERB_HUMAN | P78330 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:222
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
           SERB_HUMAN     4 HSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKLLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE 225
               SCOP domains d1l8lb_ B: Phosphoserine phosphatase                                                                                                                                                                                           SCOP domains
               CATH domains 1l8lB01                   1l8lB02 B:30-80,B:135-146                          1l8lB01 B:4-29,B:81-134,B:147-225                     1l8lB02     1l8lB01 B:4-29,B:81-134,B:147-225  [code=3.40.50.1000, no name defined]         CATH domains
           Pfam domains (1) ----------Hydrolase-1l8lB01 B:14-191                                                                                                                                                        ---------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Hydrolase-1l8lB02 B:14-191                                                                                                                                                        ---------------------------------- Pfam domains (2)
         Sec.struct. author ............eeee.........hhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeeeeehhhhhhhhhhh......eeee..eee...........hhhhh..hhhhhhhhhhhhhh...eeee..hhhhhh......eee.......hhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------N-------------------T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6c  PDB: B:4-47 UniProt: 1-47        --------------------------------------------Exon 1.8b  PDB: B:92-141 UniProt: 92-141          -------------------------------------------------Exon 1.10c  PDB: B:191-225          Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.7b  PDB: B:47-92 UniProt: 47-92        ------------------------------------------------Exon 1.9b  PDB: B:141-190 UniProt: 141-190        ----------------------------------- Transcript 1 (2)
                 1l8l B   4 HSELRKLFYSADAVCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQVQRLIAEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNGEYAGFDETQPTAESGGKGKVIKFLKEKFHFKKIIMIGDGATDMEACPPADAFIGFGGNVIRQQVKDNAKWYITDFVELLGELEE 225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

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: HAD-like (349)

Superfamily: HAD-like (349)

Family: Phosphoserine phosphatase (9)

Protein domain: Phosphoserine phosphatase (9)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d1l8la_	A:
1b	d1l8lb_	B:

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=3.40.50.1000, no name defined] (211)

Human (Homo sapiens) (42)

1a	1l8lA01	A:4-29,A:81-134,A:147-225
1b	1l8lB01	B:4-29,B:81-134,B:147-225

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: Phosphoserine phosphatase; domain 2 (9)

Human (Homo sapiens) (3)

2a	1l8lA02	A:30-80,A:135-146
2b	1l8lB02	B:30-80,B:135-146

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Hydrolase (64)

Homo sapiens (Human) (6)

1a	Hydrolase-1l8lB01	B:14-191
1b	Hydrolase-1l8lB02	B:14-191

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SERB_HUMAN | P78330)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004647	phosphoserine phosphatase activity	Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0006564	L-serine biosynthetic process	The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
	GO:0006563	L-serine metabolic process	The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	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:0009612	response to mechanical stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	GO:0031667	response to nutrient levels	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
	GO:0033574	response to testosterone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.

Asymmetric/Biological Unit
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	1l8l
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	SERB_HUMAN \| P78330	:	1l8o 1nnl

1l8o	1L8O CONTATINS CRYSTAL STRUCTURE OF THE SAME PROTEIN COMPLEX WITH PO4 AND SER

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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