3PZS - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF A PYRIDOXAMINE KINASE FROM YERSINIA PESTIS CO92

Authors :   J. S. Brunzelle, Z. Wawrzak, M. Kudritska, O. Onopriyenko, A. Savchenk W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)

Date :   14 Dec 10 (Deposition) - 16 Mar 11 (Release) - 16 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

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

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Pyridoxamine Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Brunzelle, Z. Wawrzak, M. Kudritska, O. Onopriyenko, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of A Pyridoxamine Kinase From Yersinia Pestis Co92
To Be Published
PubMed: search

Molecule 1 - PYRIDOXAMINE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIPL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PDXY, Y1967, YPO2368, YP_2154
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	214092
	Strain	:	CO92
	Synonym	:	PM KINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 27)

No.	Name	Count	Type	Full Name
1	BME	6	Ligand/Ion	BETA-MERCAPTOETHANOL
2	MSE	17	Mod. Amino Acid	SELENOMETHIONINE
3	NA	2	Ligand/Ion	SODIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:189 , CYS A:192 , GLU A:194 , HOH A:351 , HOH A:378 , HOH A:388	BINDING SITE FOR RESIDUE NA A 287
02	AC2	SOFTWARE	VAL A:219 , GLY A:220 , VAL A:221 , GLY A:222 , ASP A:223 , HOH A:375 , HOH A:549 , HOH A:556	BINDING SITE FOR RESIDUE SO4 A 288
03	AC3	SOFTWARE	GLY A:14 , GLU A:262 , GLN A:266 , HOH A:315 , HOH B:418	BINDING SITE FOR RESIDUE BME A 289
04	AC4	SOFTWARE	PHE A:40 , TRP A:49 , CYS A:52 , VAL A:53 , HIS A:189 , ALA A:190 , ASP A:191	BINDING SITE FOR RESIDUE BME A 290
05	AC5	SOFTWARE	CYS A:171 , ALA A:200	BINDING SITE FOR RESIDUE BME A 291
06	AC6	SOFTWARE	CYS A:192 , ARG A:208 , HOH A:525	BINDING SITE FOR RESIDUE BME A 292
07	AC7	SOFTWARE	HIS B:189 , CYS B:192 , GLU B:194 , HOH B:332 , HOH B:369 , HOH B:425	BINDING SITE FOR RESIDUE NA B 287
08	AC8	SOFTWARE	VAL B:219 , GLY B:220 , VAL B:221 , GLY B:222 , ASP B:223 , HOH B:341 , HOH B:381 , HOH B:401	BINDING SITE FOR RESIDUE SO4 B 288
09	AC9	SOFTWARE	HIS B:48 , TRP B:49 , CYS B:192 , CYS B:207 , ARG B:208 , PRO B:209 , HOH B:421	BINDING SITE FOR RESIDUE BME B 289
10	BC1	SOFTWARE	TRP A:33 , HOH A:347 , GLY B:14 , HIS B:15 , GLU B:264 , GLN B:266 , HOH B:313 , HOH B:346	BINDING SITE FOR RESIDUE BME B 290

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

(no "Cis Peptide Bond" information available for 3PZS)

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

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

(no "Exon" information available for 3PZS)

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:285
 aligned with PDXY_YERPE | Q7CIR8 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:285
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281     
           PDXY_YERPE     2 KNILSIQSHVVFGHAGNSAAEFPMRRMGVNVWPLNTVQFSNHTQYGHWTGCVMPASHLTDIVQGIADIDRLKDCDAVLSGYIGSPEQGSHILAAVAQVKQANPDAWYFCDPVMGHPEKGCIVAPGVAEFFCNEALPASDMIAPNLLELEQLSGERVENVEQAVQVARSLCARGPKVVLVKHLSRAGYHADCFEMLLVTADDAWHICRPLVDFGKRQPVGVGDLTSGLLLVNLLKGEPLDKALEHVTAAVYEVMLKTQEMGEYELQVVAAQETIVTPICQFTAVRL 286
               SCOP domains d3pzsa_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..hhhhh...eee.hhhhhhhhhhhhhhh.hhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeee....ee...ee..hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhh....eeee..hhhhh....eeeeeee....eeeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pzs A   2 KNILSIQSHVVFGHAGNSAAEFPmRRmGVNVWPLNTVQFSNHTQYGHWTGCVmPASHLTDIVQGIADIDRLKDCDAVLSGYIGSPEQGSHILAAVAQVKQANPDAWYFCDPVmGHPEKGCIVAPGVAEFFCNEALPASDmIAPNLLELEQLSGERVENVEQAVQVARSLCARGPKVVLVKHLSRAGYHADCFEmLLVTADDAWHICRPLVDFGKRQPVGVGDLTSGLLLVNLLKGEPLDKALEHVTAAVYEVmLKTQEmGEYELQVVAAQETIVTPICQFTAVRL 286
                                    11        21   |  | 31        41        51  |     61        71        81        91       101       111  |    121       131       141       151       161       171       181       191   |   201       211       221       231       241       251  |    261       271       281     
                                                  25-MSE                       54-MSE                                                     114-MSE                    141-MSE                                               195-MSE                                                    254-MSE |                          
                                                     28-MSE                                                                                                                                                                                                                                 260-MSE

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with PDXY_YERPE | Q7CIR8 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:286
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280      
           PDXY_YERPE     1 MKNILSIQSHVVFGHAGNSAAEFPMRRMGVNVWPLNTVQFSNHTQYGHWTGCVMPASHLTDIVQGIADIDRLKDCDAVLSGYIGSPEQGSHILAAVAQVKQANPDAWYFCDPVMGHPEKGCIVAPGVAEFFCNEALPASDMIAPNLLELEQLSGERVENVEQAVQVARSLCARGPKVVLVKHLSRAGYHADCFEMLLVTADDAWHICRPLVDFGKRQPVGVGDLTSGLLLVNLLKGEPLDKALEHVTAAVYEVMLKTQEMGEYELQVVAAQETIVTPICQFTAVRL 286
               SCOP domains d3pzsb_ B: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------Phos_pyr_kin-3pzsB01 B:42-268                                                                                                                                                                                                      ------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------Phos_pyr_kin-3pzsB02 B:42-268                                                                                                                                                                                                      ------------------ Pfam domains (2)
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..hhhhh...eee.hhhhhhhhhhhhhhh.hhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeee....ee...ee....hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeee..hhhhh....eeeeeee....eeeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pzs B   1 mKNILSIQSHVVFGHAGNSAAEFPmRRmGVNVWPLNTVQFSNHTQYGHWTGCVmPASHLTDIVQGIADIDRLKDCDAVLSGYIGSPEQGSHILAAVAQVKQANPDAWYFCDPVmGHPEKGCIVAPGVAEFFCNEALPASDmIAPNLLELEQLSGERVENVEQAVQVARSLCARGPKVVLVKHLSRAGYHADCFEmLLVTADDAWHICRPLVDFGKRQPVGVGDLTSGLLLVNLLKGEPLDKALEHVTAAVYEVmLKTQEmGEYELQVVAAQETIVTPICQFTAVRL 286
                            |       10        20    |  |30        40        50   |    60        70        80        90       100       110   |   120       130       140|      150       160       170       180       190    |  200       210       220       230       240       250   |   260       270       280      
                            1-MSE                  25-MSE                       54-MSE                                                     114-MSE                    141-MSE                                               195-MSE                                                    254-MSE |                          
                                                      28-MSE                                                                                                                                                                                                                                 260-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: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: PfkB-like kinase (20)

Protein domain: automated matches (10)

Yersinia pestis [TaxId: 214092] (1)

1a	d3pzsa_	A:
1b	d3pzsb_	B:

(no "CATH Domain" information available for 3PZS)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ribokinase (55)

Family: Phos_pyr_kin (7)

Yersinia pestis (1)

1a	Phos_pyr_kin-3pzsB01	B:42-268
1b	Phos_pyr_kin-3pzsB02	B:42-268

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDXY_YERPE | Q7CIR8)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
	GO:0008478	pyridoxal kinase activity	Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0009443	pyridoxal 5'-phosphate salvage	Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
	GO:0042816	vitamin B6 metabolic process	The chemical reactions and pathways involving any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BME	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pzs)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3pzs
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PDXY_YERPE \| Q7CIR8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.1.35
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PDXY_YERPE \| Q7CIR8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3PZS)

(no "Related Entries Specified in the PDB File" available for 3PZS)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 27)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File