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(-) Description

Title :  CRYSTAL STRUCTURE OF A RIBOKINASE-LIKE SUPERFAMILY PROTEIN (EF1790) FROM ENTEROCOCCUS FAECALIS V583 AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  29 Aug 07  (Deposition) - 11 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Putative Kinase In The Ribokinase-Like Superfamily, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Kinase In The Ribokinase-Like Superfamily From Enterococcus Faecalis V583 (Np_815490. 1) At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - YJEF-RELATED PROTEIN
    Atcc: 700802
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_815490.1, EF_1790
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: V583

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 28)

Asymmetric Unit (4, 28)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3MG2Ligand/IonMAGNESIUM ION
4MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 46)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO18Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
4MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:373 , HOH B:419 , HOH B:420 , HOH B:431 , HOH B:462 , HOH B:512BINDING SITE FOR RESIDUE MG B 292
02AC2SOFTWAREHOH A:405 , HOH A:515 , HOH A:547 , HOH A:551 , HOH A:554BINDING SITE FOR RESIDUE MG A 292
03AC3SOFTWAREASN A:34 , ARG A:35 , HOH A:340BINDING SITE FOR RESIDUE CL A 293
04AC4SOFTWAREGLY B:213 , GLY B:215 , ASP B:216 , HOH B:522BINDING SITE FOR RESIDUE CL B 293
05AC5SOFTWAREHIS A:69 , ALA A:75 , TYR B:37 , GLY B:38 , GLY B:39 , ALA B:40 , EDO B:296BINDING SITE FOR RESIDUE CL B 294
06AC6SOFTWARETYR B:269 , LYS B:272BINDING SITE FOR RESIDUE EDO B 295
07AC7SOFTWAREHIS A:153 , THR A:211 , GLY A:213 , THR A:214 , GLY A:215 , ASP A:216 , LYS B:22BINDING SITE FOR RESIDUE EDO A 294
08AC8SOFTWARETYR A:269 , LYS A:272BINDING SITE FOR RESIDUE EDO A 295
09AC9SOFTWAREGLU A:74 , MSE A:76 , ALA B:40 , MSE B:43 , ASP B:216 , CL B:294 , HOH B:372 , HOH B:522BINDING SITE FOR RESIDUE EDO B 296
10BC1SOFTWAREGLN B:122 , LYS B:147 , HOH B:553BINDING SITE FOR RESIDUE EDO B 297
11BC2SOFTWAREGLU A:146 , GLN A:177 , GLY A:181 , THR A:183 , HIS A:195 , ALA A:196 , ILE A:233 , HOH A:558BINDING SITE FOR RESIDUE EDO A 296
12BC3SOFTWARESER B:136 , GLN B:137 , ARG B:159 , HIS B:162 , HOH B:545 , HOH B:591BINDING SITE FOR RESIDUE EDO B 298
13BC4SOFTWAREGLU B:146 , GLY B:181 , SER B:182 , THR B:183 , HIS B:195 , ALA B:196 , ILE B:233 , EDO B:300BINDING SITE FOR RESIDUE EDO B 299
14BC5SOFTWAREGLU B:146 , LYS B:147 , PRO B:231 , EDO B:299 , HOH B:583BINDING SITE FOR RESIDUE EDO B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R3B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R3B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R3B)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YJEF_C_3PS51383 YjeF C-terminal domain profile.NNRD_ENTFA5-273
 		  2A:5-273
B:5-273
2YJEF_C_1PS01049 YjeF C-terminal domain signature 1.NNRD_ENTFA95-105
 		  2A:95-105
B:95-105
3YJEF_C_2PS01050 YjeF C-terminal domain signature 2.NNRD_ENTFA212-222
 		  2A:212-222
B:212-222
Biological Unit 1 (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YJEF_C_3PS51383 YjeF C-terminal domain profile.NNRD_ENTFA5-273
 		  4A:5-273
B:5-273
2YJEF_C_1PS01049 YjeF C-terminal domain signature 1.NNRD_ENTFA95-105
 		  4A:95-105
B:95-105
3YJEF_C_2PS01050 YjeF C-terminal domain signature 2.NNRD_ENTFA212-222
 		  4A:212-222
B:212-222

(-) Exons   (0, 0)

(no "Exon" information available for 2R3B)

(-) 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:283
 aligned with NNRD_ENTFA | Q833Y3 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:283
                                   1                                                                                                                                                                                                                                                                                   
                                   | 3        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   
           NNRD_ENTFA     - -------MRYLSKDILEEVITQRPSDSYKSNFGRVVLIGGNRQYGGAIIMSTEACINSGAGLTTVITDVKNHGPLHARCPEAMVVGFEETVLLTNVVEQADVILIGPGLGLDATAQQILKMVLAQHQKQQWLIIDGSAITLFSQGNFSLTYPEKVVFTPHQMEWQRLSHLPIEQQTLANNQRQQAKLGSTIVLKSHRTTIFHAGEPFQNTGGNPGMATGGTGDTLAGIIAGFLAQFKPTIETIAGAVYLHSLIGDDLAKTDYVVLPTKISQALPTYMKKYAQP 276
               SCOP domains d2r3ba_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------2r3bA01 A:2-276  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.hhhhhhhhh.......hhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eee...hhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhh....eeeeehhhhhhhhhh.....hhh.eeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhh.eeee.....eee.....ee....hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------YJEF_C_3  PDB: A:5-273 UniProt: 5-273                                                                                                                                                                                                                                        --- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------YJEF_C_1   ----------------------------------------------------------------------------------------------------------YJEF_C_2   ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r3b A  -6 ENLYFQGmRYLSKDILEEVITQRPSDSYKSNFGRVVLIGGNRQYGGAIImSTEACINSGAGLTTVITDVKNHGPLHARCPEAmVVGFEETVLLTNVVEQADVILIGPGLGLDATAQQILKmVLAQHQKQQWLIIDGSAITLFSQGNFSLTYPEKVVFTPHQmEWQRLSHLPIEQQTLANNQRQQAKLGSTIVLKSHRTTIFHAGEPFQNTGGNPGmATGGTGDTLAGIIAGFLAQFKPTIETIAGAVYLHSLIGDDLAKTDYVVLPTKISQALPTYmKKYAQP 276
                                   | 3        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   
                                   1-MSE                                    43-MSE                           76-MSE                               114-MSE                                  155-MSE                                               209-MSE                                                      270-MSE  


Chain B from PDB  Type:PROTEIN  Length:284
 aligned with NNRD_ENTFA | Q833Y3 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:284
                                    1                                                                                                                                                                                                                                                                                   
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    
           NNRD_ENTFA     - --------MRYLSKDILEEVITQRPSDSYKSNFGRVVLIGGNRQYGGAIIMSTEACINSGAGLTTVITDVKNHGPLHARCPEAMVVGFEETVLLTNVVEQADVILIGPGLGLDATAQQILKMVLAQHQKQQWLIIDGSAITLFSQGNFSLTYPEKVVFTPHQMEWQRLSHLPIEQQTLANNQRQQAKLGSTIVLKSHRTTIFHAGEPFQNTGGNPGMATGGTGDTLAGIIAGFLAQFKPTIETIAGAVYLHSLIGDDLAKTDYVVLPTKISQALPTYMKKYAQP 276
               SCOP domains d2r3bb_ B: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------2r3bB01 B:2-276  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.hhhhhhhhh.......hhhhh.eeeee.....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eee...hhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhh....eeeeehhhhhhhhhh.....hhh.eeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhh.eeee.....eee.....ee....hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------YJEF_C_3  PDB: B:5-273 UniProt: 5-273                                                                                                                                                                                                                                        --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------YJEF_C_1   ----------------------------------------------------------------------------------------------------------YJEF_C_2   ------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r3b B  -7 HENLYFQGmRYLSKDILEEVITQRPSDSYKSNFGRVVLIGGNRQYGGAIImSTEACINSGAGLTTVITDVKNHGPLHARCPEAmVVGFEETVLLTNVVEQADVILIGPGLGLDATAQQILKmVLAQHQKQQWLIIDGSAITLFSQGNFSLTYPEKVVFTPHQmEWQRLSHLPIEQQTLANNQRQQAKLGSTIVLKSHRTTIFHAGEPFQNTGGNPGmATGGTGDTLAGIIAGFLAQFKPTIETIAGAVYLHSLIGDDLAKTDYVVLPTKISQALPTYmKKYAQP 276
                                    |2        12        22        32        42|       52        62        72   |    82        92       102       112 |     122       132       142       152  |    162       172       182       192       202      |212       222       232       242       252       262       272    
                                    1-MSE                                    43-MSE                           76-MSE                               114-MSE                                  155-MSE                                               209-MSE                                                      270-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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R3B)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NNRD_ENTFA | Q833Y3)
molecular function
    GO:0052855    ADP-dependent NAD(P)H-hydrate dehydratase activity    Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ADP = AMP + 3 H(+) + NADH + phosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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:0046496    nicotinamide nucleotide metabolic process    The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide.

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  NNRD_ENTFA | Q833Y3
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NNRD_ENTFA | Q833Y3: 2r3e

(-) Related Entries Specified in the PDB File

2r3e CRYSTAL STRUCTURE OF A PUTATIVE KINASE IN THE RIBOKINASE- LIKE SUPERFAMILY FROM ENTEROCOCCUS FAECALIS V583 (NP_ 815490.1), TETRAGONAL FORM.