3JYF - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF A 2,3-CYCLIC NUCLEOTIDE 2-PHOSPHODIESTERASE/3-NUCLEOTIDASE BIFUNCTIONAL PERIPLASMIC PRECURSOR PROTEIN FROM KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE MGH 78578

Authors :   Y. Fan, L. Volkart, G. Cobb, A. Joachimiak, Midwest Center For Struc Genomics (Mcsg)

Date :   21 Sep 09 (Deposition) - 29 Sep 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.43

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

Keywords :   Apc63187. 2, Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578, 2, 3- Cyclic Nucleotide 2-Phosphodiesterase, 3-Nucleotidase, Bifunctional Periplasmic Precursor Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Metal-Binding, Nucleotide-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Fan, L. Volkart, G. Cobb, A. Joachimiak
The Crystal Structure Of A 2, 3-Cyclic Nucleotide 2-Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578
To Be Published
PubMed: search

Molecule 1 - 2',3'-CYCLIC NUCLEOTIDE 2'-PHOSPHODIESTERASE/3'- NUCLEOTIDASE BIFUNCTIONAL PERIPLASMIC PROTEIN
	Atcc	:	700721
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19
	Expression System Strain	:	PPK1037
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEQUENCE DATABASE RESIDUES 16-354
	Gene	:	CPDB, KPN78578_45340, KPN_04607
	Organism Scientific	:	KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE
	Organism Taxid	:	272620
	Strain	:	MGH 78578

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 43)

No.	Name	Count	Type	Full Name
1	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	9	Ligand/Ion	GLYCEROL
3	MN	4	Ligand/Ion	MANGANESE (II) ION
4	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	3	Ligand/Ion	SULFATE ION
6	TAM	1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Biological Unit 1 (4, 22)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	6	Ligand/Ion	GLYCEROL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	3	Ligand/Ion	SULFATE ION
6	TAM	-1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Biological Unit 2 (4, 17)

No.	Name	Count	Type	Full Name
1	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	-1	Ligand/Ion	SULFATE ION
6	TAM	1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Biological Unit 3 (4, 44)

No.	Name	Count	Type	Full Name
1	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	GOL	12	Ligand/Ion	GLYCEROL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	6	Ligand/Ion	SULFATE ION
6	TAM	-1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:16 , HIS A:18 , ASP A:61 , HIS A:244 , MN A:342 , HOH A:517	BINDING SITE FOR RESIDUE MN A 340
02	AC2	SOFTWARE	ASP A:61 , ASN A:101 , HIS A:102 , ASN A:105 , TRP A:172 , HIS A:242 , MN A:342 , GOL A:350 , HOH A:357 , HOH A:495 , HOH A:517 , HOH A:625 , HOH A:628 , HOH A:633	BINDING SITE FOR RESIDUE EPE A 341
03	AC3	SOFTWARE	ASP A:61 , ASN A:101 , HIS A:210 , HIS A:242 , MN A:340 , EPE A:341	BINDING SITE FOR RESIDUE MN A 342
04	AC4	SOFTWARE	PRO A:195 , GLU A:196 , LYS A:200 , HOH A:395	BINDING SITE FOR RESIDUE GOL A 343
05	AC5	SOFTWARE	LYS A:78 , GLU A:79 , LYS A:113	BINDING SITE FOR RESIDUE GOL A 344
06	AC6	SOFTWARE	ARG A:10 , VAL A:51 , ASP A:284 , LYS A:300 , HOH A:544	BINDING SITE FOR RESIDUE GOL A 345
07	AC7	SOFTWARE	ARG A:48 , ASN A:93 , HOH A:482 , HOH A:521	BINDING SITE FOR RESIDUE GOL A 346
08	AC8	SOFTWARE	LYS A:134 , ARG A:191 , GLN A:231 , PRO A:233 , HOH A:538	BINDING SITE FOR RESIDUE SO4 A 347
09	AC9	SOFTWARE	LYS A:256 , GLY A:257 , HOH A:491 , HOH A:518 , LYS B:256	BINDING SITE FOR RESIDUE SO4 A 348
10	BC1	SOFTWARE	ARG A:334	BINDING SITE FOR RESIDUE SO4 A 349
11	BC2	SOFTWARE	GLN A:64 , HIS A:102 , EPE A:341 , HOH A:486 , HOH A:628	BINDING SITE FOR RESIDUE GOL A 350
12	BC3	SOFTWARE	GLY A:107 , LEU A:108 , ASP A:109 , HOH A:361	BINDING SITE FOR RESIDUE GOL A 351
13	BC4	SOFTWARE	ASP B:61 , ASN B:101 , HIS B:210 , HIS B:242 , MN B:341 , EPE B:342	BINDING SITE FOR RESIDUE MN B 340
14	BC5	SOFTWARE	ASP B:16 , HIS B:18 , ASP B:61 , HIS B:244 , MN B:340 , HOH B:459	BINDING SITE FOR RESIDUE MN B 341
15	BC6	SOFTWARE	ASN B:101 , HIS B:102 , ASN B:105 , GLY B:152 , GLN B:153 , TRP B:172 , HIS B:242 , MN B:340 , HOH B:435 , HOH B:436 , HOH B:459 , HOH B:545	BINDING SITE FOR RESIDUE EPE B 342
16	BC7	SOFTWARE	HIS B:112 , TYR B:122 , PHE B:137 , THR B:138 , HOH B:512 , HOH B:543	BINDING SITE FOR RESIDUE TAM B 343
17	BC8	SOFTWARE	GLU B:188 , ARG B:191 , TYR B:218	BINDING SITE FOR RESIDUE GOL B 344
18	BC9	SOFTWARE	ARG B:146 , PRO B:167 , THR B:171 , HOH B:535	BINDING SITE FOR RESIDUE GOL B 345
19	CC1	SOFTWARE	ARG B:48 , ASN B:93 , LYS B:174 , HOH B:411 , HOH B:437 , HOH B:457	BINDING SITE FOR RESIDUE GOL B 346

(no "SS Bond" information available for 3JYF)

Asymmetric Unit

No.	Residues
1	Phe A:247	-	Pro A:248
2	Phe B:247	-	Pro B:248

(no "SAP(SNP)/Variant" information available for 3JYF)

(no "PROSITE Motif" information available for 3JYF)

(no "Exon" information available for 3JYF)

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
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Chain A from PDB  Type:PROTEIN  Length:336
 aligned with A6THC4_KLEP7 | A6THC4 from UniProtKB/TrEMBL  Length:647

    Alignment length:336
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348      
         A6THC4_KLEP7    19 AATVDLRIMETTDLHSNMMDFDYYKDAATEKFGLVRTASLIEQARAEVKNSVLVDNGDVIQGSPLGDYMAAKGLKEGDVHPVYKAMNTLNYAVGNLGNHEFNYGLDFLHKALAGAKFPYVNANIIDAKTGKPMFTPYLIQDTRVVDSDGQIHTLRIGYIGFVPPQIMTWDKANLNGKVTVNDITETARKYIPEMRAKGADVVVVVAHSGLSADPYQAMAENSVYYLSQVPGVDAIMFGHAHAVFPGKDFANIKGADIAKGTLNGVPAVMPGMWGDHLGVVDLVLNNDSGKWQVTQSKAEARPIYDAVAKKSLAAEDGKLVSVLKADHDATREFVSK 354
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3jyfA00 A:4-339  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeee.........ee....ee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhh......hhhhhhhh.....eee.hhhhhh.hhhhhhhhhhh....ee...eee..........eeeeeeeee.....eeeeeeeeeee...hhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh...eeeeee...............hhhhhh......eeee.....ee.hhhhh....ee....ee..eeeeee.....eeeeeeeeee......eeeeeeeeeee.ee....ee....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jyf A   4 AATVDLRImETTDLHSNmmDFDYYKDAATEKFGLVRTASLIEQARAEVKNSVLVDNGDVIQGSPLGDYmAAKGLKEGDVHPVYKAmNTLNYAVGNLGNHEFNYGLDFLHKALAGAKFPYVNANIIDAKTGKPmFTPYLIQDTRVVDSDGQIHTLRIGYIGFVPPQImTWDKANLNGKVTVNDITETARKYIPEmRAKGADVVVVVAHSGLSADPYQAmAENSVYYLSQVPGVDAImFGHAHAVFPGKDFANIKGADIAKGTLNGVPAVmPGmWGDHLGVVDLVLNNDSGKWQVTQSKAEARPIYDAVAKKSLAAEDGKLVSVLKADHDATREFVSK 339
                                    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       323       333      
                                   12-MSE   21-MSE                                             72-MSE           89-MSE                                        136-MSE                           170-MSE                    197-MSE                 221-MSE           239-MSE                          272-MSE                                                               
                                             22-MSE                                                                                                                                                                                                                                                      275-MSE

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with A6THC4_KLEP7 | A6THC4 from UniProtKB/TrEMBL  Length:647

    Alignment length:335
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348     
         A6THC4_KLEP7    19 AATVDLRIMETTDLHSNMMDFDYYKDAATEKFGLVRTASLIEQARAEVKNSVLVDNGDVIQGSPLGDYMAAKGLKEGDVHPVYKAMNTLNYAVGNLGNHEFNYGLDFLHKALAGAKFPYVNANIIDAKTGKPMFTPYLIQDTRVVDSDGQIHTLRIGYIGFVPPQIMTWDKANLNGKVTVNDITETARKYIPEMRAKGADVVVVVAHSGLSADPYQAMAENSVYYLSQVPGVDAIMFGHAHAVFPGKDFANIKGADIAKGTLNGVPAVMPGMWGDHLGVVDLVLNNDSGKWQVTQSKAEARPIYDAVAKKSLAAEDGKLVSVLKADHDATREFVS 353
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3jyfB00 B:4-338  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) -----Metallophos-3jyfB01 B:9-246                                                                                                                                                                                                                   -------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Metallophos-3jyfB02 B:9-246                                                                                                                                                                                                                   -------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeeee.........ee....ee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhh......hhhhhhhh.....eee.hhhhhh.hhhhhhhhhhhh...ee...eee..........eeeeeeeee.....eeeeeeeeeee...hhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh...eeeeee...............hhhhhh......eee......ee.hhhhh....ee....ee..eeeeee.....eeeeeeeeee......eeeeeeeeeee.ee....ee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jyf B   4 AATVDLRImETTDLHSNmmDFDYYKDAATEKFGLVRTASLIEQARAEVKNSVLVDNGDVIQGSPLGDYmAAKGLKEGDVHPVYKAmNTLNYAVGNLGNHEFNYGLDFLHKALAGAKFPYVNANIIDAKTGKPmFTPYLIQDTRVVDSDGQIHTLRIGYIGFVPPQImTWDKANLNGKVTVNDITETARKYIPEmRAKGADVVVVVAHSGLSADPYQAmAENSVYYLSQVPGVDAImFGHAHAVFPGKDFANIKGADIAKGTLNGVPAVmPGmWGDHLGVVDLVLNNDSGKWQVTQSKAEARPIYDAVAKKSLAAEDGKLVSVLKADHDATREFVS 338
                                    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       323       333     
                                   12-MSE   21-MSE                                             72-MSE           89-MSE                                        136-MSE                           170-MSE                    197-MSE                 221-MSE           239-MSE                          272-MSE                                                              
                                             22-MSE                                                                                                                                                                                                                                                      275-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 '\|'

(no "SCOP Domain" information available for 3JYF)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Purple Acid Phosphatase; chain A, domain 2 (87)

Homologous Superfamily: [code=3.60.21.10, no name defined] (83)

Pneumoniae mgh 78578 (Klebsiella pneumoniae subsp) (1)

1a	3jyfB00	B:4-338
1b	3jyfA00	A:4-339

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Calcineurin (56)

Family: Metallophos (45)

Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (1)

1a	Metallophos-3jyfB01	B:9-246
1b	Metallophos-3jyfB02	B:9-246

Asymmetric Unit(hide GO term definitions)

Chain A,B (A6THC4_KLEP7 | A6THC4)

molecular function
	GO:0008663	2',3'-cyclic-nucleotide 2'-phosphodiesterase activity	Catalysis of the reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate.
	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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0009166	nucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:247 - Pro A:248	[ RasMol ]
		Phe B:247 - Pro B:248	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 43)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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