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(-) Description

Title :  MONOCLINIC CRYSTAL STRUCTURE OF HUMAN PANTOTHENATE KINASE 1 ALPHA
 
Authors :  X. Guan, W. Tempel, B. Hong, A. K. Wernimont, C. H. Arrowsmith, A. M. Edwa C. Bountra, J. Weigelt, H. Park, Structural Genomics Consortium (
Date :  28 Jun 11  (Deposition) - 20 Jul 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics Consortium, Sgc, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Guan, W. Tempel, B. Hong, A. K. Wernimont, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, H. Park
Monoclinic Crystal Structure Of Human Pantothenate Kinase 1 Alpha
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PANTOTHENATE KINASE 1
    ChainsA, B
    EC Number2.7.1.33
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidBL21-V2R
    Expression System StrainPET28-LIC
    Expression System Taxid562
    FragmentUNP RESIDUES 231-597
    GenePANK1, PANK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHPANK, HPANK1, PANTOTHENIC ACID KINASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1ACO2Ligand/IonACETYL COENZYME *A
2ARS6Ligand/IonARSENIC
3CL5Ligand/IonCHLORIDE ION
4UNX6Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:397BINDING SITE FOR RESIDUE ARS A 2397
02AC2SOFTWARECYS A:301BINDING SITE FOR RESIDUE ARS A 2301
03AC3SOFTWAREGLY A:341 , SER A:417 , GLY A:418 , VAL A:419 , SER A:420 , ARG A:432 , THR A:436 , HOH A:6056 , HOH A:6094 , ILE B:478 , TYR B:479 , TYR B:483 , PHE B:486 , ALA B:492 , VAL B:493 , ALA B:494 , ASN B:524 , PHE B:565 , TRP B:566 , HOH B:6139BINDING SITE FOR RESIDUE ACO A 1001
04AC4SOFTWARECYS A:337 , HIS A:359BINDING SITE FOR RESIDUE ARS A 2337
05AC5SOFTWARECYS A:385BINDING SITE FOR RESIDUE ARS A 2385
06AC6SOFTWAREGLY A:244 , GLY A:245 , THR A:246 , LEU A:247BINDING SITE FOR RESIDUE CL A 3001
07AC7SOFTWAREGLY A:580 , TYR A:581 , PHE A:582BINDING SITE FOR RESIDUE CL A 3002
08AC8SOFTWARETYR A:479 , ALA A:492 , VAL A:493 , ALA A:494 , MET A:501 , ASN A:524 , TYR A:561 , PHE A:565 , TRP A:566 , GLY B:244 , GLY B:245 , GLY B:341 , GLY B:416 , SER B:417 , GLY B:418 , VAL B:419 , SER B:420 , ARG B:432 , THR B:436 , ASN B:547 , HOH B:6031 , HOH B:6131 , HOH B:6144BINDING SITE FOR RESIDUE ACO B 1001
09AC9SOFTWARECYS B:301BINDING SITE FOR RESIDUE ARS B 2301
10BC1SOFTWARECYS B:385 , LEU B:576BINDING SITE FOR RESIDUE ARS B 2385
11BC2SOFTWAREGLY B:580 , TYR B:581 , PHE B:582 , HOH B:6150BINDING SITE FOR RESIDUE CL B 3597
12BC3SOFTWAREPHE A:486 , LYS B:431 , ARG B:432BINDING SITE FOR RESIDUE CL B 3598
13BC4SOFTWARECYS B:301BINDING SITE FOR RESIDUE CL B 3599

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:236 -Pro A:237
2Tyr A:408 -Pro A:409
3Phe B:236 -Pro B:237
4Tyr B:408 -Pro B:409

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003075341ENSE00001263347chr10:91405215-91404357859PANK1_HUMAN1-2352352A:233-235
B:232-235
3
4
1.7aENST000003075347aENSE00001007094chr10:91371805-91371453353PANK1_HUMAN235-3521182A:235-352
B:235-352
118
118
1.8aENST000003075348aENSE00001007098chr10:91359262-91359009254PANK1_HUMAN353-437852A:353-437 (gaps)
B:353-437
85
85
1.9ENST000003075349ENSE00000986468chr10:91353746-91353570177PANK1_HUMAN437-496602A:437-496
B:437-496
60
60
1.10ENST0000030753410ENSE00000932806chr10:91353077-91352954124PANK1_HUMAN496-537422A:496-537
B:496-537
42
42
1.11ENST0000030753411ENSE00001685161chr10:91348534-91348409126PANK1_HUMAN538-579422A:538-579
B:538-579
42
42
1.12aENST0000030753412aENSE00001456068chr10:91344222-913427491474PANK1_HUMAN580-598192A:580-593
B:580-594
14
15

(-) Sequences/Alignments

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:358
 aligned with PANK1_HUMAN | Q8TE04 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:361
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592 
          PANK1_HUMAN   233 RPPFPWFGMDIGGTLVKLVYFEPKDITAEEEQEEVENLKSIRKYLTSNTAYGKTGIRDVHLELKNLTMCGRKGNLHFIRFPSCAMHRFIQMGSEKNFSSLHTTLCATGGGAFKFEEDFRMIADLQLHKLDELDCLIQGLLYVDSVGFNGKPECYYFENPTNPELCQKKPYCLDNPYPMLLVNMGSGVSILAVYSKDNYKRVTGTSLGGGTFLGLCCLLTGCETFEEALEMAAKGDSTNVDKLVKDIYGGDYERFGLQGSAVASSFGNMMSKEKRDSISKEDLARATLVTITNNIGSIARMCALNENIDRVVFVGNFLRINMVSMKLLAYAMDFWSKGQLKALFLEHEGYFGAVGALLELFK 593
               SCOP domains d3smpa1 A:233-381 Pantothenate kinase 1, PANK1                                                                                                       d3smpa2 A:382-593 Pant   othenate kinase 1, PANK1                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.ee...eee.hhhheeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhh......eeeee........eeeee.---...eeeeee...eeeeeeee..eeeeeeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eehhhhhh..hhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhh..hhhhhhhhhhhhhhh.......ee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1---------------------------------------------------------------------------------------------------------------------Exon 1.8a  PDB: A:353-437 (gaps) UniProt: 353-437                                    ----------------------------------------------------------Exon 1.10  PDB: A:496-537 UniProt: 496-537Exon 1.11  PDB: A:538-579 UniProt: 538-579Exon 1.12a     Transcript 1 (1)
           Transcript 1 (2) --Exon 1.7a  PDB: A:235-352 UniProt: 235-352                                                                            ------------------------------------------------------------------------------------Exon 1.9  PDB: A:437-496 UniProt: 437-496                   ------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3smp A 233 RPPFPWFGMDIGGTLVKLVYFEPKDITAEEEQEEVENLKSIRKYLTSNTAYGKTGIRDVHLELKNLTMCGRKGNLHFIRFPSCAMHRFIQMGSEKNFSSLHTTLCATGGGAFKFEEDFRMIADLQLHKLDELDCLIQGLLYVDSVGFNGKPECYYFENPTNPELCQKKPYC---PYPMLLVNMGSGVSILAVYSKDNYKRVTGTSLGGGTFLGLCCLLTGCETFEEALEMAAKGDSTNVDKLVKDIYGGDYERFGLQGSAVASSFGNMMSKEKRDSISKEDLARATLVTITNNIGSIARMCALNENIDRVVFVGNFLRINMVSMKLLAYAMDFWSKGQLKALFLEHEGYFGAVGALLELFK 593
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402|   |  412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592 
                                                                                                                                                                                                    403 407                                                                                                                                                                                          

Chain B from PDB  Type:PROTEIN  Length:363
 aligned with PANK1_HUMAN | Q8TE04 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:363
                                   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591   
          PANK1_HUMAN   232 NRPPFPWFGMDIGGTLVKLVYFEPKDITAEEEQEEVENLKSIRKYLTSNTAYGKTGIRDVHLELKNLTMCGRKGNLHFIRFPSCAMHRFIQMGSEKNFSSLHTTLCATGGGAFKFEEDFRMIADLQLHKLDELDCLIQGLLYVDSVGFNGKPECYYFENPTNPELCQKKPYCLDNPYPMLLVNMGSGVSILAVYSKDNYKRVTGTSLGGGTFLGLCCLLTGCETFEEALEMAAKGDSTNVDKLVKDIYGGDYERFGLQGSAVASSFGNMMSKEKRDSISKEDLARATLVTITNNIGSIARMCALNENIDRVVFVGNFLRINMVSMKLLAYAMDFWSKGQLKALFLEHEGYFGAVGALLELFKM 594
               SCOP domains d3smpb1 B:232-381 Pantothenate kinase 1, PANK1                                                                                                        d3smpb2 B:382-594 Pantothenate kinase 1, PANK1                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee...eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.ee...eee.hhhheeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhh......eeeee........eeee........eeeeee...eeeeeeee..eeeeeeee..hhhhhhhhhhhhhh..hhhhhhhhhh..hhhhh.eehhhhhh..hhhhh.....eee.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhh..hhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1 ---------------------------------------------------------------------------------------------------------------------Exon 1.8a  PDB: B:353-437 UniProt: 353-437                                           ----------------------------------------------------------Exon 1.10  PDB: B:496-537 UniProt: 496-537Exon 1.11  PDB: B:538-579 UniProt: 538-579Exon 1.12a      Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.7a  PDB: B:235-352 UniProt: 235-352                                                                            ------------------------------------------------------------------------------------Exon 1.9  PDB: B:437-496 UniProt: 437-496                   -------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3smp B 232 NRPPFPWFGMDIGGTLVKLVYFEPKDITAEEEQEEVENLKSIRKYLTSNTAYGKTGIRDVHLELKNLTMCGRKGNLHFIRFPSCAMHRFIQMGSEKNFSSLHTTLCATGGGAFKFEEDFRMIADLQLHKLDELDCLIQGLLYVDSVGFNGKPECYYFENPTNPELCQKKPYCLDNPYPMLLVNMGSGVSILAVYSKDNYKRVTGTSLGGGTFLGLCCLLTGCETFEEALEMAAKGDSTNVDKLVKDIYGGDYERFGLQGSAVASSFGNMMSKEKRDSISKEDLARATLVTITNNIGSIARMCALNENIDRVVFVGNFLRINMVSMKLLAYAMDFWSKGQLKALFLEHEGYFGAVGALLELFKM 594
                                   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591   

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SMP)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PANK1_HUMAN | Q8TE04)
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: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:0004594    pantothenate kinase activity    Catalysis of the reaction: ATP + pantothenate = ADP + D-4'-phosphopantothenate.
    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:0015937    coenzyme A biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
    GO:0009108    coenzyme biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzymes, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    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.
cellular component
    GO:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    GO:0030118    clathrin coat    A membrane coat found on coated pits and some coated vesicles; consists of polymerized clathrin triskelions, each comprising three clathrin heavy chains and three clathrin light chains, linked to the membrane via one of the AP adaptor complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.

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        PANK1_HUMAN | Q8TE042i7n

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