1L7O - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE IN APO FORM

Authors :   W. Wang, H. S. Cho, R. Kim, J. Jancarik, H. Yokota, H. H. Nguyen, I. V. Grig D. E. Wemmer, S. H. Kim, Berkeley Structural Genomics Center (Bsg

Date :   16 Mar 02 (Deposition) - 19 Jun 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Rossmann Fold, Beta-Hairpin, Four-Helix Bundle, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Wang, H. S. Cho, R. Kim, J. Jancarik, H. Yokota, H. H. Nguyen, I. V. Grigoriev, D. E. Wemmer, S. H. Kim
Structural Characterization Of The Reaction Pathway In Phosphoserine Phosphatase: Crystallographic "Snapshots" Of Intermediate States.
J. Mol. Biol. V. 319 421 2002
PubMed-ID: 12051918 | Reference-DOI: 10.1016/S0022-2836(02)00324-8

Molecule 1 - PHOSPHOSERINE PHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	B834(DE3)/PSJS1244
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MJ1594
	Mutation	:	YES
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	PSP, O-PHOSPHOSERINE PHOSPHOHYDROLASE, PSPASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:197 , GLU A:199 , CYS B:697 , GLU B:699	BINDING SITE FOR RESIDUE ZN B 301
2	AC2	SOFTWARE	GLU A:79 , GLU A:146 , GLU A:149 , ACY A:312 , HOH A:2045	BINDING SITE FOR RESIDUE ZN A 302
3	AC3	SOFTWARE	ACY B:311 , GLU B:579 , GLU B:646 , GLU B:649	BINDING SITE FOR RESIDUE ZN B 303
4	AC4	SOFTWARE	ZN B:303 , GLU B:579 , GLY B:580 , GLU B:583 , GLU B:646 , HOH B:2060	BINDING SITE FOR RESIDUE ACY B 311
5	AC5	SOFTWARE	GLU A:79 , GLY A:80 , GLU A:83 , GLU A:146 , ZN A:302 , HOH A:2045	BINDING SITE FOR RESIDUE ACY A 312

(no "SS Bond" information available for 1L7O)

(no "Cis Peptide Bond" information available for 1L7O)

(no "SAP(SNP)/Variant" information available for 1L7O)

(no "PROSITE Motif" information available for 1L7O)

(no "Exon" information available for 1L7O)

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:200
 aligned with SERB_METJA | Q58989 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:208
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        
           SERB_METJA     4 KKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 211
               SCOP domains d1l7oa_ A: Phosphoserine phosphatase                                                                                                                                                                             SCOP domains
               CATH domains 1l7oA01      1l7oA02 A:17-77 Phospho        serine phosphatase; domain 2  1l7oA01 A:4-16,A:78-209  [code=3.40.50.1000, no name defined]                                                                       -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........hhhhhhhhhh.hhhhhhh..--------hhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeee......hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeeee..hhhhhh...eee...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l7o A   4 KKKLILFNFDSTLVNNETIDEIAREAGVEEEVKKIT--------NFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISmFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 211
                                    13        23        33     |   -    |   53        63        73        83        93       103       113       123       133       143       153       163       173|      183       193       203        
                                                              39       48                                                                                                                           174-MSE

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with SERB_METJA | Q58989 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:208
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        
           SERB_METJA     4 KKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 211
               SCOP domains d1l7ob_ B: Phosphoserine phosphatase                                                                                                                                                                             SCOP domains
               CATH domains 1l7oB01      1l7oB02 B:517-577 Phosphoserine phosphatase; domain 2        1l7oB01 B:504-516,B:578-709  [code=3.40.50.1000, no name defined]                                                                   -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhh..eeeeeeeeee..eeeeeee......hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeeee..hhhhhh...eee...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l7o B 504 KKKLILFNFDSTLVNNETIDEIAREAGVEEEVKKITKEAmEGKLNFEQSLRKRVSLLKDLPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISmFKKAGLKIAFCAKPILKEKADICIEKRDLREILKYIK 711
                                   513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673|      683       693       703        
                                                                 543-MSE                                                                                                                            674-MSE

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

Methanococcus jannaschii [TaxId: 2190] (6)

1a	d1l7oa_	A:
1b	d1l7ob_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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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)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (3)

1a	1l7oA01	A:4-16,A:78-209
1b	1l7oB01	B:504-516,B:578-709

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: Phosphoserine phosphatase; domain 2 (9)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (3)

2a	1l7oB02	B:517-577
2b	1l7oA02	A:17-77

(no "Pfam Domain" information available for 1L7O)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SERB_METJA | Q58989)

molecular function
	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.
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: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.
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
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	1l7o
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	3.1.3.3
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	SERB_METJA \| Q58989
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UniProtKB/Swiss-Prot
	SERB_METJA \| Q58989	:	1f5s 1j97 1l7m 1l7n 1l7p

1j97	PSP-BEF3 COMPLEX STRUCTRE
1l7m	HIGH RESOLUTION LIGANDED STRUCTURE OF PHOSPHOSERINE PHOSPHATASE (PI COMPLEX)
1l7n	TRANSITION STATE ANALOGUE OF PHOSPHOSERINE PHOSPHATASE (ALUMINUM FLUORIDE COMPLEX)
1l7p	SUBSTRATE BOUND PHOSPHOSERINE PHOSPHATASE COMPLEX STRUCTURE RELATED ID: BSGCAIR30380 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (5, 5)

SS Bonds (0, 0)

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