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Title :   STRUCTURE OF THE METAL-FREE FORM OF THE DEOXY-D-MANNOSE-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE (YRBI) FROM HAEMOPHILUS INFLUENZAE (HI1679)

Authors :   K. Lim, O. Herzberg, Structure 2 Function Project (S2F)

Date :   21 May 01 (Deposition) - 27 Feb 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Hi1679, Structural Genomics, Kdo 8-P Phosphatase, Structure 2 Function Project, S2F, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Parsons, K. Lim, A. Tempczyk, W. Krajewski, E. Eisenstein, O. Herzberg
From Structure To Function: Yrbi From Haemophilus Influenza (Hi1679) Is A Phosphatase.
Proteins V. 46 393 2002
PubMed-ID: 11835514 | Reference-DOI: 10.1002/PROT.10057

Molecule 1 - DEOXY-D-MANNOSE-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE
	Chains	:	A, B, C, D
	EC Number	:	3.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST14-HI1679
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PDEST14
	Gene	:	HI1679
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE RD
	Organism Taxid	:	71421
	Strain	:	KW20
	Synonym	:	YRBI, KDO 8-P PHOSPHATASE, HI1679

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 29)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	28	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE D:33	BINDING SITE FOR RESIDUE GOL D 200

(no "SS Bond" information available for 1J8D)

(no "Cis Peptide Bond" information available for 1J8D)

(no "SAP(SNP)/Variant" information available for 1J8D)

(no "PROSITE Motif" information available for 1J8D)

(no "Exon" information available for 1J8D)

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:180
 aligned with KDSC_HAEIN | P45314 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           KDSC_HAEIN     1 MQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREMSDMILQAQGKSSVFDTAQGFLKSVKSMGQ 180
               SCOP domains d1j8da_ A: Probable phosphatase YrbI                                                                                                                                                 SCOP domains
               CATH domains -1j8dA00 A:2-180  [code=3.40.50.1000, no name defined]                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh..eeee.........eeeee..eeeeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhh...ee.......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j8d A   1 mQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKmLmDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLmKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREmSDmILQAQGKSSVFDTAQGFLKSVKSmGQ 180
                            |       10        20        30        40     | |50        60        70        80        90 |     100       110       120       130       140       150|  |   160       170       180
                            |                                           46-MSE                                        92-MSE                                                    151-MSE                    178-MSE
                            1-MSE                                         48-MSE                                                                                                   154-MSE

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with KDSC_HAEIN | P45314 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           KDSC_HAEIN     1 MQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREMSDMILQAQGKSSVFDTAQGFLKSVKSMGQ 180
               SCOP domains d1j8db_ B: Probable phosphatase YrbI                                                                                                                                                 SCOP domains
               CATH domains -1j8dB00 B:2-180  [code=3.40.50.1000, no name defined]                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh.eeee.........eeeee..eeeeeeeehhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhh...ee.......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j8d B   1 mQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKmLmDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLmKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREmSDmILQAQGKSSVFDTAQGFLKSVKSmGQ 180
                            |       10        20        30        40     | |50        60        70        80        90 |     100       110       120       130       140       150|  |   160       170       180
                            |                                           46-MSE                                        92-MSE                                                    151-MSE                    178-MSE
                            1-MSE                                         48-MSE                                                                                                   154-MSE

Chain C from PDB  Type:PROTEIN  Length:180
 aligned with KDSC_HAEIN | P45314 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           KDSC_HAEIN     1 MQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREMSDMILQAQGKSSVFDTAQGFLKSVKSMGQ 180
               SCOP domains d1j8dc_ C: Probable phosphatase YrbI                                                                                                                                                 SCOP domains
               CATH domains -1j8dC00 C:2-180  [code=3.40.50.1000, no name defined]                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh.eeee.........eeeee..eeeeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhh...ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j8d C   1 mQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKmLmDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLmKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREmSDmILQAQGKSSVFDTAQGFLKSVKSmGQ 180
                            |       10        20        30        40     | |50        60        70        80        90 |     100       110       120       130       140       150|  |   160       170       180
                            |                                           46-MSE                                        92-MSE                                                    151-MSE                    178-MSE
                            1-MSE                                         48-MSE                                                                                                   154-MSE

Chain D from PDB  Type:PROTEIN  Length:180
 aligned with KDSC_HAEIN | P45314 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           KDSC_HAEIN     1 MQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREMSDMILQAQGKSSVFDTAQGFLKSVKSMGQ 180
               SCOP domains d1j8dd_ D: Probable phosphatase YrbI                                                                                                                                                 SCOP domains
               CATH domains -1j8dD00 D:2-180  [code=3.40.50.1000, no name defined]                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh...eeee.........eeeee..eeeeeeeehhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeee....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhheeee....hhhhhh...ee.......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j8d D   1 mQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKmLmDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLmKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREmSDmILQAQGKSSVFDTAQGFLKSVKSmGQ 180
                            |       10        20        30        40     | |50        60        70        80        90 |     100       110       120       130       140       150|  |   160       170       180
                            |                                           46-MSE                                        92-MSE                                                    151-MSE                    178-MSE
                            1-MSE                                         48-MSE                                                                                                   154-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/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: Probable phosphatase YrbI (2)

Protein domain: Probable phosphatase YrbI (2)

Haemophilus influenzae, HI1679 [TaxId: 727] (2)

1a	d1j8da_	A:
1b	d1j8db_	B:
1c	d1j8dc_	C:
1d	d1j8dd_	D:

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)

Haemophilus influenzae rd kw20. Organism_taxid: 71421. Strain: kw20. (2)

1a	1j8dA00	A:2-180
1b	1j8dB00	B:2-180
1c	1j8dC00	C:2-180
1d	1j8dD00	D:2-180

(no "Pfam Domain" information available for 1J8D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (KDSC_HAEIN | P45314)

molecular function
	GO:0019143	3-deoxy-manno-octulosonate-8-phosphatase activity	Catalysis of the reaction: 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate.
	GO:0008781	N-acylneuraminate cytidylyltransferase activity	Catalysis of the reaction: CTP + N-acylneuraminate = diphosphate + CMP-N-acylneuraminate.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0009103	lipopolysaccharide biosynthetic process	The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	KDSC_HAEIN \| P45314	:	1k1e 4hgp

1k1e	1K1E IS THE COBALT BOUND FORM OF THE HI1679 STRUCTURE DETERMINED TO 1.67 ANGSTROM RELATED ID: HI1679 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 29)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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