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Title :   CRYSTAL STRUCTURE ANALYSIS OF URIDYLATE KINASE FROM NEISSERIA MENINGITIDIS

Authors :   D. Kumaran, S. Swaminathan, S. K. Burley, New York Sgx Research Cen Structural Genomics (Nysgxrc)

Date :   20 Dec 04 (Deposition) - 15 Feb 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,C  (3x)
Biol. Unit 2: B  (4x)
Biol. Unit 3: A,C  (1x)
Biol. Unit 4: B  (2x)
Biol. Unit 5: B  (6x)

Keywords :   Alpha/Beta/Alpha Fold, Kinase, Hexamer, Structural Genomics, Protein Structure Initiative, Psi, New York Sgx Research Center For Structural Genomics, Nysgxrc, T1843, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Kumaran, S. Swaminathan
Crystal Structure Analysis Of Uridylate Kinase From Neisseria Meningitidis
To Be Published
PubMed: search

Molecule 1 - URIDYLATE KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PYRH
	Organism Scientific	:	NEISSERIA MENINGITIDIS
	Organism Taxid	:	487
	Synonym	:	UK, URIDINE MONOPHOSPHATE KINASE, UMP KINASE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (3x)	:	A		C
Biological Unit 2 (4x)	:		B
Biological Unit 3 (1x)	:	A		C
Biological Unit 4 (2x)	:		B
Biological Unit 5 (6x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 37)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL
3	MSE	33	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 75)

No.	Name	Count	Type	Full Name
1	FMT	3	Ligand/Ion	FORMIC ACID
2	GOL	6	Ligand/Ion	GLYCEROL
3	MSE	66	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 48)

No.	Name	Count	Type	Full Name
1	FMT	-1	Ligand/Ion	FORMIC ACID
2	GOL	4	Ligand/Ion	GLYCEROL
3	MSE	44	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (3, 25)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	22	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 24)

No.	Name	Count	Type	Full Name
1	FMT	-1	Ligand/Ion	FORMIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	22	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 5 (2, 72)

No.	Name	Count	Type	Full Name
1	FMT	-1	Ligand/Ion	FORMIC ACID
2	GOL	6	Ligand/Ion	GLYCEROL
3	MSE	66	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:107 , GLN A:112 , THR A:138 , HOH A:255 , THR C:138 , ASN C:140 , HOH C:270	BINDING SITE FOR RESIDUE FMT A 253
2	AC2	SOFTWARE	LYS A:15 , SER A:17 , THR A:145 , HOH A:260 , HOH A:270	BINDING SITE FOR RESIDUE GOL A 250
3	AC3	SOFTWARE	LYS B:15 , SER B:17 , THR B:145 , HOH B:256 , HOH B:269 , HOH B:277	BINDING SITE FOR RESIDUE GOL B 251
4	AC4	SOFTWARE	LYS C:15 , SER C:17 , THR C:165 , HOH C:262	BINDING SITE FOR RESIDUE GOL C 252

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

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

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

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

(no "Exon" information available for 1YBD)

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:236
 aligned with PYRH_NEIMB | P65932 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:236
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233      
           PYRH_NEIMB     4 QIKYKRVLLKLSGESLMGSDPFGINHDTIVQTVGEIAEVVKMGVQVGIVVGGGNIFRGVSAQAGSMDRATADYMGMMATVMNALALKDAFETLGIKARVQSALSMQQIAETYARPKAIQYLEEGKVVIFAAGTGNPFFTTDTAAALRGAEMNCDVMLKATNVDGVYTADPKKDPSATRYETITFDEALLKNLKVMDATAFALCRERKLNIVVFGIAKEGSLKRVITGEDEGTLVHC 239
               SCOP domains d1ybda1 A:6-241 Uridylate kinase PyrH                                                                                                                                                                                                        SCOP domains
               CATH domains 1ybdA00 A:6-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhh......hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeee.........hhhhh.......eeehhhhhhh.....hhhhhhhhhhh...eeee.....hhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybd A   6 QIKYKRVLLKLSGESLmGSDPFGINHDTIVQTVGEIAEVVKmGVQVGIVVGGGNIFRGVSAQAGSmDRATADYmGmmATVmNALALKDAFETLGIKARVQSALSmQQIAETYARPKAIQYLEEGKVVIFAAGTGNPFFTTDTAAALRGAEmNCDVmLKATNVDGVYTADPKKDPSATRYETITFDEALLKNLKVmDATAFALCRERKLNIVVFGIAKEGSLKRVITGEDEGTLVHC 241
                                    15      | 25        35        45 |      55        65     |  75   | || 85|       95       105    |  115       125       135       145       155|    | 165       175       185       195    |  205       215       225       235      
                                           22-MSE                   47-MSE                  71-MSE  79-MSE  |                     110-MSE                                       156-MSE|                                    200-MSE                                     
                                                                                                      81-MSE|                                                                        161-MSE                                                                            
                                                                                                       82-MSE                                                                                                                                                           
                                                                                                           86-MSE

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with PYRH_NEIMB | P65932 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:236
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233      
           PYRH_NEIMB     4 QIKYKRVLLKLSGESLMGSDPFGINHDTIVQTVGEIAEVVKMGVQVGIVVGGGNIFRGVSAQAGSMDRATADYMGMMATVMNALALKDAFETLGIKARVQSALSMQQIAETYARPKAIQYLEEGKVVIFAAGTGNPFFTTDTAAALRGAEMNCDVMLKATNVDGVYTADPKKDPSATRYETITFDEALLKNLKVMDATAFALCRERKLNIVVFGIAKEGSLKRVITGEDEGTLVHC 239
               SCOP domains d1ybdb_ B: Uridylate kinase PyrH                                                                                                                                                                                                             SCOP domains
               CATH domains 1ybdB00 B:6-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhh.......hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee....................eeehhhhhhh.....hhhhhhhhhhhh..eeeee....hhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybd B   6 QIKYKRVLLKLSGESLmGSDPFGINHDTIVQTVGEIAEVVKmGVQVGIVVGGGNIFRGVSAQAGSmDRATADYmGmmATVmNALALKDAFETLGIKARVQSALSmQQIAETYARPKAIQYLEEGKVVIFAAGTGNPFFTTDTAAALRGAEmNCDVmLKATNVDGVYTADPKKDPSATRYETITFDEALLKNLKVmDATAFALCRERKLNIVVFGIAKEGSLKRVITGEDEGTLVHC 241
                                    15      | 25        35        45 |      55        65     |  75   | || 85|       95       105    |  115       125       135       145       155|    | 165       175       185       195    |  205       215       225       235      
                                           22-MSE                   47-MSE                  71-MSE  79-MSE  |                     110-MSE                                       156-MSE|                                    200-MSE                                     
                                                                                                      81-MSE|                                                                        161-MSE                                                                            
                                                                                                       82-MSE                                                                                                                                                           
                                                                                                           86-MSE

Chain C from PDB  Type:PROTEIN  Length:236
 aligned with PYRH_NEIMB | P65932 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:236
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233      
           PYRH_NEIMB     4 QIKYKRVLLKLSGESLMGSDPFGINHDTIVQTVGEIAEVVKMGVQVGIVVGGGNIFRGVSAQAGSMDRATADYMGMMATVMNALALKDAFETLGIKARVQSALSMQQIAETYARPKAIQYLEEGKVVIFAAGTGNPFFTTDTAAALRGAEMNCDVMLKATNVDGVYTADPKKDPSATRYETITFDEALLKNLKVMDATAFALCRERKLNIVVFGIAKEGSLKRVITGEDEGTLVHC 239
               SCOP domains d1ybdc_ C: Uridylate kinase PyrH                                                                                                                                                                                                             SCOP domains
               CATH domains 1ybdC00 C:6-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                        CATH domains
           Pfam domains (1) ----AA_kinase-1ybdC01 C:10-219                                                                                                                                                                                        ---------------------- Pfam domains (1)
           Pfam domains (2) ----AA_kinase-1ybdC02 C:10-219                                                                                                                                                                                        ---------------------- Pfam domains (2)
           Pfam domains (3) ----AA_kinase-1ybdC03 C:10-219                                                                                                                                                                                        ---------------------- Pfam domains (3)
         Sec.struct. author .....eeeeeehhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee....................eeehhhhhhh.....hhhhhhhhhhhh..eeeee....hhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybd C   6 QIKYKRVLLKLSGESLmGSDPFGINHDTIVQTVGEIAEVVKmGVQVGIVVGGGNIFRGVSAQAGSmDRATADYmGmmATVmNALALKDAFETLGIKARVQSALSmQQIAETYARPKAIQYLEEGKVVIFAAGTGNPFFTTDTAAALRGAEmNCDVmLKATNVDGVYTADPKKDPSATRYETITFDEALLKNLKVmDATAFALCRERKLNIVVFGIAKEGSLKRVITGEDEGTLVHC 241
                                    15      | 25        35        45 |      55        65     |  75   | || 85|       95       105    |  115       125       135       145       155|    | 165       175       185       195    |  205       215       225       235      
                                           22-MSE                   47-MSE                  71-MSE  79-MSE  |                     110-MSE                                       156-MSE|                                    200-MSE                                     
                                                                                                      81-MSE|                                                                        161-MSE                                                                            
                                                                                                       82-MSE                                                                                                                                                           
                                                                                                           86-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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Carbamate kinase-like (63)

Superfamily: Carbamate kinase-like (63)

Family: PyrH-like (22)

Protein domain: Uridylate kinase PyrH (6)

Neisseria meningitidis [TaxId: 487] (1)

1a	d1ybda1	A:6-241
1b	d1ybdb_	B:
1c	d1ybdc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Carbamate kinase (24)

Homologous Superfamily: [code=3.40.1160.10, no name defined] (24)

Neisseria meningitidis. Organism_taxid: 487. (1)

1a	1ybdA00	A:6-241
1b	1ybdB00	B:6-241
1c	1ybdC00	C:6-241

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: AA_kinase] (20)

Family: AA_kinase (20)

Neisseria meningitidis serogroup B (1)

1a	AA_kinase-1ybdC01	C:10-219
1b	AA_kinase-1ybdC02	C:10-219
1c	AA_kinase-1ybdC03	C:10-219

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PYRH_NEIMB | P65932)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0033862	UMP kinase activity	Catalysis of the reaction: ATP + UMP = ADP + UDP.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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: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.
	GO:0009041	uridylate kinase activity	Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
biological process
	GO:0044210	'de novo' CTP biosynthetic process	The chemical reactions and pathways resulting in the formation of cytidine 5'-triphosphate (CTP) from simpler components.
	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.
	GO:0046939	nucleotide phosphorylation	The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
	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:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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