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(-) Description

Title :  INSIGHTS INTO THE UBIQUITIN TRANSFER CASCADE FROM THE REFINED STRUCTURE OF THE ACTIVATING ENZYME FOR NEDD8
 
Authors :  H. Walden, M. S. Podgorski, B. A. Schulman
Date :  28 Jan 05  (Deposition) - 08 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ubiquitin, Nedd8, E1, Appbp1, Uba3, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Walden, M. S. Podgorski, B. A. Schulman
Insights Into The Ubiquitin Transfer Cascade From The Refined Structure Of The Activating Enzyme For Nedd8
Nature V. 422 330 2003
PubMed-ID: 12646924  |  Reference-DOI: 10.1038/NATURE01456
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMYLOID PROTEIN-BINDING PROTEIN 1
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneAPPBP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAMYLOID BETA PRECURSOR PROTEIN-BINDING PROTEIN 1, 59 KDA, APP-BP1, PROTOONCOGENE PROTEIN 1, HPP1
 
Molecule 2 - UBIQUITIN-ACTIVATING ENZYME E1C
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneUBE1C, UBA3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEDD8-ACTIVATING ENZYME E1C, UBIQUITIN-ACTIVATING ENZYME 3 HOMOLOG

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:199 , CYS B:202 , CYS B:343 , CYS B:346BINDING SITE FOR RESIDUE ZN B 443
2AC2SOFTWARECYS D:199 , CYS D:202 , CYS D:343 , CYS D:346BINDING SITE FOR RESIDUE ZN D 443

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052435S101FULA1_HUMANPolymorphism363212A/CS101F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052435S101FULA1_HUMANPolymorphism363212AS101F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052435S101FULA1_HUMANPolymorphism363212CS101F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_ACTIVAT_2PS00865 Ubiquitin-activating enzyme active site.UBA3_HUMAN235-243
 
  2B:214-222
D:214-222
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_ACTIVAT_2PS00865 Ubiquitin-activating enzyme active site.UBA3_HUMAN235-243
 
  1B:214-222
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_ACTIVAT_2PS00865 Ubiquitin-activating enzyme active site.UBA3_HUMAN235-243
 
  1-
D:214-222

(-) Exons   (36, 72)

Asymmetric Unit (36, 72)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002908101aENSE00001857882chr16:66864900-66864750151ULA1_HUMAN1-18182A:6-18
C:9-18
13
10
1.3aENST000002908103aENSE00001739042chr16:66860683-66860580104ULA1_HUMAN18-53362A:18-53
C:18-53
36
36
1.4ENST000002908104ENSE00001779668chr16:66860486-6686042661ULA1_HUMAN53-73212A:53-73
C:53-73
21
21
1.5ENST000002908105ENSE00001624314chr16:66858788-6685875831ULA1_HUMAN73-83112A:73-83
C:73-83
11
11
1.6ENST000002908106ENSE00001761968chr16:66857503-6685743272ULA1_HUMAN84-107242A:84-107
C:84-107
24
24
1.7ENST000002908107ENSE00001104193chr16:66857209-6685713080ULA1_HUMAN108-134272A:108-134
C:108-134
27
27
1.8ENST000002908108ENSE00001104205chr16:66855462-66855353110ULA1_HUMAN134-171382A:134-171
C:134-171
38
38
1.9ENST000002908109ENSE00001104202chr16:66852540-66852431110ULA1_HUMAN171-207372A:171-207
C:171-207
37
37
1.10ENST0000029081010ENSE00001104208chr16:66851390-6685132863ULA1_HUMAN208-228212A:208-228
C:208-228
21
21
1.11ENST0000029081011ENSE00001104214chr16:66850931-6685086864ULA1_HUMAN229-250222A:229-250
C:229-250
22
22
1.12ENST0000029081012ENSE00001104186chr16:66850575-6685048492ULA1_HUMAN250-280312A:250-280
C:250-280
31
31
1.13ENST0000029081013ENSE00001139971chr16:66847749-6684769060ULA1_HUMAN281-300202A:281-300
C:281-300
20
20
1.14ENST0000029081014ENSE00001139961chr16:66847600-66847467134ULA1_HUMAN301-345452A:301-345
C:301-345
45
45
1.15ENST0000029081015ENSE00001139952chr16:66844675-6684460076ULA1_HUMAN345-370262A:345-370
C:345-370
26
26
1.16ENST0000029081016ENSE00001046614chr16:66844316-6684427740ULA1_HUMAN371-384142A:371-384
C:371-384
14
14
1.17ENST0000029081017ENSE00001046603chr16:66842978-6684289287ULA1_HUMAN384-413302A:384-413
C:384-413
30
30
1.18ENST0000029081018ENSE00001046627chr16:66842516-6684242493ULA1_HUMAN413-444322A:413-444
C:413-444
32
32
1.19ENST0000029081019ENSE00001104192chr16:66839929-66839815115ULA1_HUMAN444-482392A:444-482
C:444-482
39
39
1.20ENST0000029081020ENSE00001104217chr16:66839729-6683968050ULA1_HUMAN482-499182A:482-499
C:482-499
18
18
1.21bENST0000029081021bENSE00001907559chr16:66837021-66836778244ULA1_HUMAN499-534362A:499-534
C:499-534
36
36

2.1aENST000003610551aENSE00001864869chr3:69129559-6912948575UBA3_HUMAN1-770--
2.2aENST000003610552aENSE00001417479chr3:69129304-6912926342UBA3_HUMAN7-21150--
2.3aENST000003610553aENSE00000966869chr3:69127069-69126949121UBA3_HUMAN21-61412B:12-40
D:19-40
29
22
2.4aENST000003610554aENSE00001377164chr3:69124661-6912458181UBA3_HUMAN62-88272B:41-67
D:41-67
27
27
2.5aENST000003610555aENSE00001376644chr3:69120768-6912068683UBA3_HUMAN89-116282B:68-95
D:68-95
28
28
2.6ENST000003610556ENSE00000966872chr3:69117159-6911707981UBA3_HUMAN116-143282B:95-122
D:95-122
28
28
2.7aENST000003610557aENSE00000966873chr3:69113262-6911321944UBA3_HUMAN143-158162B:122-137
D:122-137
16
16
2.8ENST000003610558ENSE00000966874chr3:69112654-6911259065UBA3_HUMAN158-179222B:137-158
D:137-158
22
22
2.9ENST000003610559ENSE00000966875chr3:69112288-69112133156UBA3_HUMAN180-231522B:159-210
D:159-210
52
52
2.10ENST0000036105510ENSE00000966876chr3:69111330-69111228103UBA3_HUMAN232-266352B:211-245
D:211-245
35
35
2.11aENST0000036105511aENSE00000966877chr3:69111078-69110965114UBA3_HUMAN266-304392B:245-283
D:245-283
39
39
2.12ENST0000036105512ENSE00000966878chr3:69106460-6910640754UBA3_HUMAN304-322192B:283-301
D:283-301
19
19
2.13ENST0000036105513ENSE00001656120chr3:69105966-6910593037UBA3_HUMAN322-334132B:301-313
D:301-313
13
13
2.14ENST0000036105514ENSE00001685710chr3:69105844-6910576382UBA3_HUMAN334-361282B:313-340
D:313-340
28
28
2.15ENST0000036105515ENSE00001754233chr3:69105434-69105334101UBA3_HUMAN362-395342B:341-374 (gaps)
D:341-374 (gaps)
34
34
2.16ENST0000036105516ENSE00001711956chr3:69105214-6910515164UBA3_HUMAN395-416222B:374-395 (gaps)
D:374-395 (gaps)
22
22
2.17ENST0000036105517ENSE00001673741chr3:69105056-6910500255UBA3_HUMAN417-435192B:396-408 (gaps)
D:396-401 (gaps)
13
6
2.18bENST0000036105518bENSE00001518240chr3:69104676-69103881796UBA3_HUMAN435-463292B:423-437
D:425-436
15
12

(-) 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:529
 aligned with ULA1_HUMAN | Q13564 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:529
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525         
           ULA1_HUMAN     6 KLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDNALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL 534
               SCOP domains d1yova_ A: Amyloid beta precursor protein-binding protein 1, APPBP1                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1yovA01 A:6-178,A:388-534 NAD(P)-binding Rossmann-like Domain                                                                                                                -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1yovA01 A:6-178,A:388-534 NAD(P)-binding Rossmann-like Domain                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhheeee...hhhhhhhhhhhhh....eeeee.....hhhhhhhh...hhhhh..hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhh..eeeeeee..eeeeeee...eee.................hhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhh............hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....eee...hhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......eeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a    ----------------------------------Exon 1.4  PDB: A:53-7----------Exon 1.6  PDB: A:84-107 Exon 1.7  PDB: A:108-134   ------------------------------------Exon 1.9  PDB: A:171-207             Exon 1.10            Exon 1.11             ------------------------------Exon 1.13           Exon 1.14  PDB: A:301-345 UniProt: 301-345   -------------------------Exon 1.16     ----------------------------Exon 1.18  PDB: A:413-444       -------------------------------------Exon 1.20         ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3a  PDB: A:18-53             -------------------Exon 1.5   --------------------------------------------------Exon 1.8  PDB: A:134-171              ------------------------------------------------------------------------------Exon 1.12  PDB: A:250-280      ----------------------------------------------------------------Exon 1.15  PDB: A:345-370 -------------Exon 1.17  PDB: A:384-413     ------------------------------Exon 1.19  PDB: A:444-482              ----------------Exon 1.21b  PDB: A:499-534           Transcript 1 (2)
                 1yov A   6 KLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDNALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL 534
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525         

Chain B from PDB  Type:PROTEIN  Length:397
 aligned with UBA3_HUMAN | Q8TBC4 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:426
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452      
           UBA3_HUMAN    33 DWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFK 458
               SCOP domains d1yovb_ B: UBA3                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1yovB01 B:12-209,B:289-339 NAD(P)-binding Rossmann-like Domain                                                                                                                                        --1yovB02 B:212-288 Ubiquitin activating enzymes (Uba3). Chain: B, domain 2    1yovB01 B:12-209,B:289-339                         1yovB03 B:340-4      04                                          ----              --------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhh.............hhhhhhhhhh.eeee....hhhhhhhhhhh.....eeee.....hhhhhhh....hhhhh..hhhhhhhhhhhhhh.....eee..hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh..ee..ee.hhhh..eeeeeee..eeeeeee......hhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee...............ee..------..hhhhhh............ee..-----.ee....----hhhhh...--------------.............ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UBIQUITIN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.3a  PDB: B:12-40      Exon 2.4a  PDB: B:41-67    Exon 2.5a  PDB: B:68-95     --------------------------Exon 2.7a       ---------------------Exon 2.9  PDB: B:159-210 UniProt: 180-231           Exon 2.10  PDB: B:211-245          -------------------------------------Exon 2.12          -----------Exon 2.14  PDB: B:313-340   Exon 2.15  PDB: B:341-374 (gaps)  ---------------------Exon 2.17          ----------------------- Transcript 2 (1)
           Transcript 2 (2) -----------------------------------------------------------------------------------Exon 2.6  PDB: B:95-122     --------------Exon 2.8              --------------------------------------------------------------------------------------Exon 2.11a  PDB: B:245-283             -----------------Exon 2.13    ------------------------------------------------------------Exon 2.16             ------------------Exon 2.18b [INCOMPLETE]  Transcript 2 (2)
                 1yov B  12 DWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQ------LQEVLDYLTNSASLQMKSPAITAT-----RTLYLQS----EERTRPNL--------------LAVADVTTPQTVLFK 437
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351  |    361       371       381  |    391    |  401      |  -         - |     431      
                                                                                                                                                                                                                                                                                                                                                                                354    361                    384   390   396  401    408            423              

Chain C from PDB  Type:PROTEIN  Length:526
 aligned with ULA1_HUMAN | Q13564 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:526
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528      
           ULA1_HUMAN     9 KEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDNALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL 534
               SCOP domains d1yovc_ C: Amyloid beta precursor protein-binding protein 1, APPBP1                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1yovC01 C:9-178,C:388-534 NAD(P)-binding Rossmann-like Domain                                                                                                             -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1yovC01 C:9-178,C:388-534 NAD(P)-binding Rossmann-like Domain                                                                                       CATH domains
           Pfam domains (1) --------------------ThiF-1yovC01 C:29-165                                                                                                                    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------ThiF-1yovC02 C:29-165                                                                                                                    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhheeee...hhhhhhhhhhhhh....eee.......hhhhhhhh..........hhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh...eeeeeee..eeeeeee...eee.................hhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhh............hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhheee...hhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh........eeee....eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------F------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a ----------------------------------Exon 1.4  PDB: C:53-7----------Exon 1.6  PDB: C:84-107 Exon 1.7  PDB: C:108-134   ------------------------------------Exon 1.9  PDB: C:171-207             Exon 1.10            Exon 1.11             ------------------------------Exon 1.13           Exon 1.14  PDB: C:301-345 UniProt: 301-345   -------------------------Exon 1.16     ----------------------------Exon 1.18  PDB: C:413-444       -------------------------------------Exon 1.20         ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.3a  PDB: C:18-53             -------------------Exon 1.5   --------------------------------------------------Exon 1.8  PDB: C:134-171              ------------------------------------------------------------------------------Exon 1.12  PDB: C:250-280      ----------------------------------------------------------------Exon 1.15  PDB: C:345-370 -------------Exon 1.17  PDB: C:384-413     ------------------------------Exon 1.19  PDB: C:444-482              ----------------Exon 1.21b  PDB: C:499-534           Transcript 1 (2)
                 1yov C   9 KEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDNALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL 534
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528      

Chain D from PDB  Type:PROTEIN  Length:382
 aligned with UBA3_HUMAN | Q8TBC4 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:418
                                    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        
           UBA3_HUMAN    40 HVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLF 457
               SCOP domains d1yovd_ D: UBA3                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1yovD01 D:19-209,D:289-339 NAD(P)-binding Rossmann-like Domain                                                                                                                                 --1yovD02 D:212-288 Ubiquitin activating enzymes (Uba3). Chain: B, domain 2    1yovD01 D:19-209,D:289-339                         1yovD03 D:340-4      00                                      -                       ------------ CATH domains
           Pfam domains (1) ----------------------------ThiF-1yovD01 D:47-192                                                                                                                             --UBA_e1_thiolCys-1yovD07 D:195-241              ------UBACT-1yovD05 D:248-314                                            --------------------------------------E2      _bind-1yovD03 D:353-43      6                                                Pfam domains (1)
           Pfam domains (2) ----------------------------ThiF-1yovD02 D:47-192                                                                                                                             --UBA_e1_thiolCys-1yovD08 D:195-241              ------UBACT-1yovD06 D:248-314                                            --------------------------------------E2      _bind-1yovD04 D:353-43      6                                                Pfam domains (2)
         Sec.struct. author .......................hhhhhh...eeee..hhhhhhhhhhhhh....eeeee.....hhhhh.............hhhhhhhhhhhhhh...eeeee..hhhhh...hhhhh.eeee...hhhhhhhhhhhhhhh..ee..ee.hhhh..eeeeeee..eeeeeee.......hhhhh.........hhhhhhh...hhhhhhhhhh..hhhhhh..............hhhhhhhhhhhhhhhh.....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh........eeee.....eeee....................------..hhhhhhhhh........ee.------....ee..-....-----------------------............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UBIQUITIN---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.3a  PDB: D:19-4Exon 2.4a  PDB: D:41-67    Exon 2.5a  PDB: D:68-95     --------------------------Exon 2.7a       ---------------------Exon 2.9  PDB: D:159-210 UniProt: 180-231           Exon 2.10  PDB: D:211-245          -------------------------------------Exon 2.12          -----------Exon 2.14  PDB: D:313-340   Exon 2.15  PDB: D:341-374 (gaps)  ---------------------Exon 2.17          ---------------------- Transcript 2 (1)
           Transcript 2 (2) ----------------------------------------------------------------------------Exon 2.6  PDB: D:95-122     --------------Exon 2.8              --------------------------------------------------------------------------------------Exon 2.11a  PDB: D:245-283             -----------------Exon 2.13    ------------------------------------------------------------Exon 2.16             ------------------Exon 2.18b [INCOMPLETE] Transcript 2 (2)
                 1yov D  19 HVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQ------LQEVLDYLTNSASLQMKSPAIT------NRTLYLQS-TSIE-----------------------VADVTTPQTVLF 436
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348     |   -  |    368       378   |     -|      398  |      -         -      |428        
                                                                                                                                                                                                                                                                                                                                                                         354    361                  382    389    396 |  |                     425           
                                                                                                                                                                                                                                                                                                                                                                                                                     398  |                                   
                                                                                                                                                                                                                                                                                                                                                                                                                        401                                   

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (3, 8)

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

(-) Pfam Domains  (4, 10)

Asymmetric Unit
(-)
Family: ThiF (14)
1aThiF-1yovD01D:47-192
1bThiF-1yovD02D:47-192
1cThiF-1yovC01C:29-165
1dThiF-1yovC02C:29-165
(-)
Family: UBACT (10)

(-) Gene Ontology  (30, 38)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (ULA1_HUMAN | Q13564)
molecular function
    GO:0019781    NEDD8 activating enzyme activity    Catalysis of the initiation of the NEDD8 (RUB1) conjugation cascade.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0008641    small protein activating enzyme activity    Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0033314    mitotic DNA replication checkpoint    A cell cycle checkpoint that acts during a mitotic cell cycle and prevents the initiation of mitosis until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome.
    GO:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0043523    regulation of neuron apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B,D   (UBA3_HUMAN | Q8TBC4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019781    NEDD8 activating enzyme activity    Catalysis of the initiation of the NEDD8 (RUB1) conjugation cascade.
    GO:0016881    acid-amino acid ligase activity    Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0016922    ligand-dependent nuclear receptor binding    Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0008641    small protein activating enzyme activity    Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
biological process
    GO:0038061    NIK/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0007113    endomitotic cell cycle    A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UBA3_HUMAN | Q8TBC41r4m 1r4n 1tt5 1y8x 2lq7 2nvu 3dbh 3dbl 3dbr 3fn1 3gzn 5jjm
        ULA1_HUMAN | Q135641r4m 1r4n 1tt5 2nvu 3dbh 3dbl 3dbr 3gzn

(-) Related Entries Specified in the PDB File

1r4m 1r4n 1tt5 1y8x