3LL3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   THE CRYSTAL STRUCTURE OF LIGAND BOUND XYLULOSE KINASE FROM LACTOBACILLUS ACIDOPHILUS

Authors :   Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   28 Jan 10 (Deposition) - 23 Mar 10 (Release) - 23 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Xylulose Kinase, 11120E1, Nysgx, Atp, Adp, Xylulose, Kinase, Transferase, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhang, S. K. Burley, S. Swaminathan
The Crystal Structure Of Xylulose Kinase From Lactobacillus Acidophilus
To Be Published
PubMed: search

Molecule 1 - GLUCONATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3(BC)
	Expression System Strain	:	BL21(DE3)CODON+RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	LBA0354
	Organism Scientific	:	LACTOBACILLUS ACIDOPHILUS
	Organism Taxid	:	1579
	Strain	:	NCFM

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 25)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	DXP	2	Ligand/Ion	1-DEOXY-D-XYLULOSE-5-PHOSPHATE
4	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
5	XUL	1	Ligand/Ion	D-XYLULOSE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:258 , THR A:259 , GLY A:298 , ILE A:299 , ASN A:302 , PRO A:315 , GLY A:399 , GLY A:400 , PHE A:401 , HOH A:572 , HOH A:581 , HOH A:650 , HOH A:656 , HOH A:703 , HOH A:723 , HOH A:733 , HOH A:760 , HOH A:842 , HOH A:847	BINDING SITE FOR RESIDUE ATP A 1760
2	AC2	SOFTWARE	HIS A:127 , ASN A:295 , GLY A:339 , GLU A:341 , ARG A:342 , ALA A:348 , HOH A:669	BINDING SITE FOR RESIDUE DXP A 3264
3	AC3	SOFTWARE	GLN A:77 , MSE A:78 , HIS A:79 , ASP A:237 , PHE A:279 , TYR A:281 , ARG A:342	BINDING SITE FOR RESIDUE XUL A 7778
4	AC4	SOFTWARE	GLY B:258 , THR B:259 , GLY B:298 , ILE B:299 , PHE B:301 , ASN B:302 , PRO B:315 , LEU B:319 , GLY B:400 , PHE B:401 , LYS B:403 , HOH B:506 , HOH B:554 , HOH B:594 , HOH B:655 , HOH B:668 , HOH B:679 , HOH B:684 , HOH B:704	BINDING SITE FOR RESIDUE ADP B 1761
5	AC5	SOFTWARE	HIS B:127 , ASN B:295 , GLY B:339 , GLY B:340 , GLU B:341 , ARG B:342 , ALA B:348 , HOH B:602	BINDING SITE FOR RESIDUE DXP B 3265

(no "SS Bond" information available for 3LL3)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:213	-	Pro A:214
2	Ala A:343	-	Pro A:344
3	Phe B:213	-	Pro B:214
4	Ala B:343	-	Pro B:344

(no "SAP(SNP)/Variant" information available for 3LL3)

(no "PROSITE Motif" information available for 3LL3)

(no "Exon" information available for 3LL3)

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:492
 aligned with Q5FM28_LACAC | Q5FM28 from UniProtKB/TrEMBL  Length:494

    Alignment length:492
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489  
         Q5FM28_LACAC     - -MKYIIGMDVGTTATKGVLYDINGKAVASVSKGYPLIQTKVGQAEEDPKLIFDAVQEIIFDLTQKIDGKIAAISWSSQMHSLIGLGSDDELLTNSITWADNCAKSIVQDAKNRGFAQQIYRKTGMPMHPMAPIYKLLWLKNKKTEVFSQAQKWIGIKEYIIFRLTGKLVTDTTMAAGTGILNLKTLTWDQELLDILKIKKEQLPKIAQPTKVIFPIKTEYVKKLGIDSDTKIILGASDGYLSTIGVNAIDSDHCALNVGTSGAIRTIVDQPKIDPSASYFCYPADKTHYLLGGPVNNGGIVFNWARQTLFDADETPQDFLDVAQTAPAGSRNLIFLPYLGGERAPIWDANARGSFVGLTRMHQKPEMARAVIEGIIFNLYDAASNLIKNTKKPVAINATGGFLKSDFVRQLCANIFNVPIVTMKEQQSGTLAAMFLARQALGLNQDLSEIGQFAQADKVYFPNPKEAATYQKLFPLYCEIRNALAASYGKFS 491
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeee....eeeeeeee...........eehhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eee.........ee......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhh..eeehhhhh............hhhhhhhhh.hhhhh.eee....ee...hhhhhhhhh.....eeeeeeehhhhhhhh.......eeeeee...eeeeeee...........eeeeee..eeeeeeee..hhhhhhhhhhhhh....hhhhhhhhhhh...hhhhheee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....hhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ll3 A   0 SLKYIIGmDVGTTATKGVLYDINGKAVASVSKGYPLIQTKVGQAEEDPKLIFDAVQEIIFDLTQKIDGKIAAISWSSQmHSLIGLGSDDELLTNSITWADNCAKSIVQDAKNRGFAQQIYRKTGmPmHPmAPIYKLLWLKNKKTEVFSQAQKWIGIKEYIIFRLTGKLVTDTTmAAGTGILNLKTLTWDQELLDILKIKKEQLPKIAQPTKVIFPIKTEYVKKLGIDSDTKIILGASDGYLSTIGVNAIDSDHCALNVGTSGAIRTIVDQPKIDPSASYFCYPADKTHYLLGGPVNNGGIVFNWARQTLFDADETPQDFLDVAQTAPAGSRNLIFLPYLGGERAPIWDANARGSFVGLTRmHQKPEmARAVIEGIIFNLYDAASNLIKNTKKPVAINATGGFLKSDFVRQLCANIFNVPIVTmKEQQSGTLAAmFLARQALGLNQDLSEIGQFAQADKVYFPNPKEAATYQKLFPLYCEIRNALAASYGKFS 491
                                   | 9        19        29        39        49        59        69        79        89        99       109       119    | |129       139       149       159       169   |   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359|     |369       379       389       399       409       419  |    429   |   439       449       459       469       479       489  
                                   7-MSE                                                                 78-MSE                                       124-MSE|                                         173-MSE                                                                                                                                                                                    360-MSE |                                                     422-MSE    433-MSE                                                      
                                                                                                                                                        126-MSE                                                                                                                                                                                                                                         366-MSE                                                                                                                         
                                                                                                                                                           129-MSE

Chain B from PDB  Type:PROTEIN  Length:490
 aligned with Q5FM28_LACAC | Q5FM28 from UniProtKB/TrEMBL  Length:494

    Alignment length:491
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490 
         Q5FM28_LACAC     1 MKYIIGMDVGTTATKGVLYDINGKAVASVSKGYPLIQTKVGQAEEDPKLIFDAVQEIIFDLTQKIDGKIAAISWSSQMHSLIGLGSDDELLTNSITWADNCAKSIVQDAKNRGFAQQIYRKTGMPMHPMAPIYKLLWLKNKKTEVFSQAQKWIGIKEYIIFRLTGKLVTDTTMAAGTGILNLKTLTWDQELLDILKIKKEQLPKIAQPTKVIFPIKTEYVKKLGIDSDTKIILGASDGYLSTIGVNAIDSDHCALNVGTSGAIRTIVDQPKIDPSASYFCYPADKTHYLLGGPVNNGGIVFNWARQTLFDADETPQDFLDVAQTAPAGSRNLIFLPYLGGERAPIWDANARGSFVGLTRMHQKPEMARAVIEGIIFNLYDAASNLIKNTKKPVAINATGGFLKSDFVRQLCANIFNVPIVTMKEQQSGTLAAMFLARQALGLNQDLSEIGQFAQADKVYFPNPKEAATYQKLFPLYCEIRNALAASYGKFS 491
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --FGGY_N-3ll3B03 B:3-244                                                                                                                                                                                                                            --------FGGY_C-3ll3B01 B:253-440                                                                                                                                                                    --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --FGGY_N-3ll3B04 B:3-244                                                                                                                                                                                                                            --------FGGY_C-3ll3B02 B:253-440                                                                                                                                                                    --------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhh....eeeeeeeee.....eee.........ee......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhh..eeehhhhh............hhhhhhhhh.hhhhh.eee....ee...hhhhhhhhh.....eee..eehhhhhhhh.......eeeeee...eeeeeee...........eeeeee..eeeeeeee..hhhhhhhhhhhhh-...hhhhhhhhhh....hhhhheee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....hhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ll3 B   1 LKYIIGmDVGTTATKGVLYDINGKAVASVSKGYPLIQTKVGQAEEDPKLIFDAVQEIIFDLTQKIDGKIAAISWSSQmHSLIGLGSDDELLTNSITWADNCAKSIVQDAKNRGFAQQIYRKTGmPmHPmAPIYKLLWLKNKKTEVFSQAQKWIGIKEYIIFRLTGKLVTDTTmAAGTGILNLKTLTWDQELLDILKIKKEQLPKIAQPTKVIFPIKTEYVKKLGIDSDTKIILGASDGYLSTIGVNAIDSDHCALNVGTSGAIRTIVDQPKIDPSASYFCYPADKTHYLLGGPVNNGGIVFNWARQTLF-ADETPQDFLDVAQTAPAGSRNLIFLPYLGGERAPIWDANARGSFVGLTRmHQKPEmARAVIEGIIFNLYDAASNLIKNTKKPVAINATGGFLKSDFVRQLCANIFNVPIVTmKEQQSGTLAAmFLARQALGLNQDLSEIGQFAQADKVYFPNPKEAATYQKLFPLYCEIRNALAASYGKFS 491
                                  | 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       290       300        |-|      320       330       340       350       360     | 370       380       390       400       410       420 |     430  |    440       450       460       470       480       490 
                                  7-MSE                                                                 78-MSE                                       124-MSE|                                         173-MSE                                                                                                                                 309 |                                              360-MSE |                                                     422-MSE    433-MSE                                                      
                                                                                                                                                       126-MSE                                                                                                                                                                                  311                                                    366-MSE                                                                                                                         
                                                                                                                                                          129-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 3LL3)

(no "CATH Domain" information available for 3LL3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Actin_ATPase (173)

Family: FGGY_C (10)

Lactobacillus acidophilus NCFM (1)

1a	FGGY_C-3ll3B01	B:253-440
1b	FGGY_C-3ll3B02	B:253-440

Family: FGGY_N (10)

Lactobacillus acidophilus NCFM (1)

2a	FGGY_N-3ll3B03	B:3-244
2b	FGGY_N-3ll3B04	B:3-244

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q5FM28_LACAC | Q5FM28)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046316	gluconokinase activity	Catalysis of the reaction: D-gluconate + ATP = 6-phospho-D-gluconate + ADP + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	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:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:343 - Pro A:344	[ RasMol ]
		Ala B:343 - Pro B:344	[ RasMol ]
		Phe A:213 - Pro A:214	[ RasMol ]
		Phe B:213 - Pro B:214	[ RasMol ]

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	3ll3
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	2.7.1.12
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	Q5FM28_LACAC \| Q5FM28	:	3gbt

3gbt	RELATED ID: NYSGXRC-11200E RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 25)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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