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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE URIDYLATE KINASE (UMP-KINASE) FROM STREPTOCOCCUS PYOGENES
 
Authors :  K. R. Rajashankar, R. Kniewel, K. Lee, C. D. Lima, S. K. Burley, New York Research Center For Structural Genomics (Nysgxrc)
Date :  01 Apr 05  (Deposition) - 19 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A,B,C  (2x)
Keywords :  Structural Genomics; Protein Structure Initiative; Nysgxrc; T1668; Pyrh; Putative Uridylate Kinase, Ump-Kinase, Psi, New York Sgx Research Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. R. Rajashankar, R. Kniewel, K. Lee, C. D. Lima
Crystal Structure Of A Putative Uridylate Kinase (Ump-Kinase) From Streptococcus Pyogenes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URIDYLATE KINASE
    Chains: A, B, C
    EC Number: 2.7.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET T7
    Expression System Strain: B834, DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PYRH
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Synonym: UK;
URIDINE MONOPHOSPHATE KINASE;
UMP KINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 36)

Asymmetric Unit (2, 36)
No.NameCountTypeFull Name
1MSE27Mod. Amino AcidSELENOMETHIONINE
2SO49Ligand/IonSULFATE ION
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (2, 11)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 72)
No.NameCountTypeFull Name
1MSE54Mod. Amino AcidSELENOMETHIONINE
2SO418Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:101 , ARG A:119 , ARG A:128 , ARG B:122 , HOH B:1024BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREARG B:101 , ARG B:119 , HIS B:123 , ARG B:128 , HOH B:1014 , ARG C:122BINDING SITE FOR RESIDUE SO4 B 1002
3AC3SOFTWAREARG A:119 , ARG A:122 , ARG C:101 , ARG C:119BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWARESER A:15 , LYS A:163 , ASN A:164BINDING SITE FOR RESIDUE SO4 A 1004
5AC5SOFTWARESER B:15 , LYS B:163 , ASN B:164 , HOH B:1040BINDING SITE FOR RESIDUE SO4 B 1005
6AC6SOFTWARESER C:15 , LYS C:163 , ASN C:164 , HOH C:1034BINDING SITE FOR RESIDUE SO4 C 1006
7AC7SOFTWARELYS A:13 , SER A:15 , GLY A:16 , GLY A:54 , GLY A:55 , THR A:143 , HOH A:1024BINDING SITE FOR RESIDUE SO4 A 1007
8AC8SOFTWARESER B:15 , GLY B:16 , GLY B:54 , GLY B:55 , THR B:143 , HOH B:1015BINDING SITE FOR RESIDUE SO4 B 1008
9AC9SOFTWARELYS C:13 , SER C:15 , GLY C:54 , GLY C:55 , THR C:143 , HOH C:1033BINDING SITE FOR RESIDUE SO4 C 1009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z9D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z9D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z9D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z9D)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z9D)

(-) Sequences/Alignments

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:238
 aligned with PYRH_STRP1 | P65938 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           PYRH_STRP1     2 EPKYQRILIKLSGEALAGEKGVGIDIPTVQAIAKEIAEVHVSGVQIALVIGGGNLWRGEPAADAGMDRVQADYTGMLGTVMNALVMADSLQHYGVDTRVQTAIPMQNVAEPYIRGRALRHLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEADAILMAKNGVDGVYNADPKKDANAVKFDELTHGEVIKRGLKIMDATASTLSMDNDIDLVVFNMNEAGNIQRVVFGEHIGTTVSNK 239
               SCOP domains d1z9da1 A:4-241 Uridylate kinase PyrH                                                                                                                                                                                                          SCOP domains
               CATH domains 1z9dA00 A:4-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhh.......hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee.....................eeehhhhhh......hhhhhhhhhhh..eeeeee....hhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9d A   4 EPKYQRILIKLSGEALAGEKGVGIDIPTVQAIAKEIAEVHVSGVQIALVIGGGNLWRGEPAADAGmDRVQADYTGmLGTVmNALVmADSLQHYGVDTRVQTAIPmQNVAEPYIRGRALRHLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEADAILmAKNGVDGVYNADPKKDANAVKFDELTHGEVIKRGLKImDATASTLSmDNDIDLVVFNmNEAGNIQRVVFGEHIGTTVSNK 241
                                    13        23        33        43        53        63     |  73     |  83|    |  93       103    |  113       123       133       143       153       163       173       183       193     | 203    |  213     | 223       233        
                                                                                            69-MSE    79-MSE|    |                108-MSE                                              161-MSE                               199-MSE  208-MSE    219-MSE                  
                                                                                                           84-MSE|                                                                                                                                                        
                                                                                                                89-MSE                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with PYRH_STRP1 | P65938 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           PYRH_STRP1     2 EPKYQRILIKLSGEALAGEKGVGIDIPTVQAIAKEIAEVHVSGVQIALVIGGGNLWRGEPAADAGMDRVQADYTGMLGTVMNALVMADSLQHYGVDTRVQTAIPMQNVAEPYIRGRALRHLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEADAILMAKNGVDGVYNADPKKDANAVKFDELTHGEVIKRGLKIMDATASTLSMDNDIDLVVFNMNEAGNIQRVVFGEHIGTTVSNK 239
               SCOP domains d1z9db_ B: Uridylate kinase PyrH                                                                                                                                                                                                               SCOP domains
               CATH domains 1z9dB00 B:4-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhh.......hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee.....................eehhhhhhh......hhhhhhhhhhh..eeeeee....hhhhhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9d B   4 EPKYQRILIKLSGEALAGEKGVGIDIPTVQAIAKEIAEVHVSGVQIALVIGGGNLWRGEPAADAGmDRVQADYTGmLGTVmNALVmADSLQHYGVDTRVQTAIPmQNVAEPYIRGRALRHLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEADAILmAKNGVDGVYNADPKKDANAVKFDELTHGEVIKRGLKImDATASTLSmDNDIDLVVFNmNEAGNIQRVVFGEHIGTTVSNK 241
                                    13        23        33        43        53        63     |  73     |  83|    |  93       103    |  113       123       133       143       153       163       173       183       193     | 203    |  213     | 223       233        
                                                                                            69-MSE    79-MSE|    |                108-MSE                                              161-MSE                               199-MSE  208-MSE    219-MSE                  
                                                                                                           84-MSE|                                                                                                                                                        
                                                                                                                89-MSE                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:238
 aligned with PYRH_STRP1 | P65938 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           PYRH_STRP1     2 EPKYQRILIKLSGEALAGEKGVGIDIPTVQAIAKEIAEVHVSGVQIALVIGGGNLWRGEPAADAGMDRVQADYTGMLGTVMNALVMADSLQHYGVDTRVQTAIPMQNVAEPYIRGRALRHLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEADAILMAKNGVDGVYNADPKKDANAVKFDELTHGEVIKRGLKIMDATASTLSMDNDIDLVVFNMNEAGNIQRVVFGEHIGTTVSNK 239
               SCOP domains d1z9dc_ C: Uridylate kinase PyrH                                                                                                                                                                                                               SCOP domains
               CATH domains 1z9dC00 C:4-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
           Pfam domains (1) ----AA_kinase-1z9dC01 C:8-218                                                                                                                                                                                          ----------------------- Pfam domains (1)
           Pfam domains (2) ----AA_kinase-1z9dC02 C:8-218                                                                                                                                                                                          ----------------------- Pfam domains (2)
           Pfam domains (3) ----AA_kinase-1z9dC03 C:8-218                                                                                                                                                                                          ----------------------- Pfam domains (3)
         Sec.struct. author .....eeeeeehhhhhh.......hhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee.....................eehhhhhhh......hhhhhhhhhhh..eeeeee....hhhhhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z9d C   4 EPKYQRILIKLSGEALAGEKGVGIDIPTVQAIAKEIAEVHVSGVQIALVIGGGNLWRGEPAADAGmDRVQADYTGmLGTVmNALVmADSLQHYGVDTRVQTAIPmQNVAEPYIRGRALRHLEKNRIVVFGAGIGSPYFSTDTTAALRAAEIEADAILmAKNGVDGVYNADPKKDANAVKFDELTHGEVIKRGLKImDATASTLSmDNDIDLVVFNmNEAGNIQRVVFGEHIGTTVSNK 241
                                    13        23        33        43        53        63     |  73     |  83|    |  93       103    |  113       123       133       143       153       163       173       183       193     | 203    |  213     | 223       233        
                                                                                            69-MSE    79-MSE|    |                108-MSE                                              161-MSE                               199-MSE  208-MSE    219-MSE                  
                                                                                                           84-MSE|                                                                                                                                                        
                                                                                                                89-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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

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

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PYRH_STRP1 | P65938)
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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