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Data and Databases

Your questions:

– Lookup

– Compare

– Predict

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Your questions

Lookup• Is the gene known for my protein (or vice versa)? • What sequence patterns are present in my protein? • Are the mutations known which cause this disease?• To what class or family does my protein belong?

Compare• Are there protein sequences in the database which resemble the protein I

cloned?• How can I optimally align the members of this protein family?• Are these two sequences similar?

Predict• Can I predict the active site residues of this enzyme?• Can I make a 3D model for my protein? Can I predict a (better) drug for

this target?• How can I improve the thermostability of this protein? (protein engineering)• How can I predict the genes located on this genome?

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Sequence similarity

MVVSGAPPAL GGGCLGTFTS LLLLASTAIL NAARIPVPPA CGKPQQLNRV VGGEDSTDSEWPWIVSIQKN GTHHCAGSLL TSRWVITAAH CFKDNLNKPY LFSVLLGAWQ LGNPGSRSQKVGVAWVEPHP VYSWKEGACA DIALVRLERS IQFSERVLPI CLPDASIHLP PNTHCWISGWGSIQDGVPLP HPQTLQKLKV PIIDSEVCSH LYWRGAGQGP ITEDMLCAGY LEGERDACLGDSGGPLMCQV DGAWLLAGII SWGEGCAERN RPGVYISLSA HRSWVEKIVQ GVQLRGRAQG

Image, you sequenced this human protein.

You know it is a serine protease.Which residues belong to the active site?Is its sequence similar to the mouse serine protease?

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Alignment

MVVSGAPPAL GGGCLGTFTS LLLLASTAIL NAARIPVPPA CGKPQQLNRV VGGEDSTDSEMMISRPPPAL GGDQFSILIL LVLLTSTAPI SAATIRVSPD CGKPQQLNRI VGGEDSMDAQ*::* .**** **. :. : *:**:*** : .** * *.* *********: ****** *:: WPWIVSIQKN GTHHCAGSLL TSRWVITAAH CFKDNLNKPY LFSVLLGAWQ LGNPGSRSQKWPWIVSILKN GSHHCAGSLL TNRWVVTAAH CFKSNMDKPS LFSVLLGAWK LGSPGPRSQK******* ** *:******** *.***:**** ***.*::** *********: **.**.**** VGVAWVEPHP VYSWKEGACA DIALVRLERS IQFSERVLPI CLPDASIHLP PNTHCWISGWVGIAWVLPHP RYSWKEGTHA DIALVRLEHS IQFSERILPI CLPDSSVRLP PKTDCWIAGW**:*** *** ******: * ********:* ******:*** ****:*::** *:*.***:** GSIQDGVPLP HPQTLQKLKV PIIDSEVCSH LYWRGAGQGP ITEDMLCAGY LEGERDACLGGSIQDGVPLP HPQTLQKLKV PIIDSELCKS LYWRGAGQEA ITEGMLCAGY LEGERDACLG********** ********** ******:*. ******** . ***.****** ********** DSGGPLMCQV DGAWLLAGII SWGEGCAERN RPGVYISLSA HRSWVEKIVQ GVQLRGRAQGDSGGPLMCQV DDHWLLTGII SWGEGCAD-D RPGVYTSLLA HRSWVQRIVQ GVQLRG----********** *. ***:*** *******: : ***** ** * *****::*** ******

=> Transfer of information

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Data & Databases

• Data in databases

what the data looks like

• Programs (tools) to search these databases

how it can be accessed

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Biological Databases

The number of databases- DBCAT lists over 1200 databases (2006)

The size of databases- Grows exponentially- EMBL database: New entries entered at 5 sec/seq!

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Database Size

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Primary and Secondary Databases

Primary databases REAL EXPERIMENTAL DATA

Biomolecular sequences or structures and associated annotation information (organism, function, mutation linked to disease, functional/structural patterns, bibliographic etc.)

Secondary databases

DERIVED INFORMATIONFruits of analyses of sequences in the primary sources (patterns, blocks, profiles etc., that represent the most conserved features of multiple alignments)

©CMBI 2008

Primary Databases

Sequence Information

• DNA: EMBL, Genbank, DDBJ• Protein: SwissProt, TREMBL, PIR

Genome Information

• EnsEMBL, TIGR rice genome, Celera, SNP databases

Structure Information

• PDB, NDB, CCDB/CSD

©CMBI 2008

Secondary Databases

Sequence-related Information-ProSite, Enzyme, REBase

Genome-related Information-OMIM, TransFac

Structure-related Information-DSSP, HSSP, FSSP, PDBFinder

Pathway Information-KEGG, Pathways

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Prosite example

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KEGG example

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Databases

Data must be in a certain format for software to recognize

Every database can have its own format but some data elements are essential for every database:

1. Unique identifier, or accession code2. Name of depositor3. Literature references4. Deposition date5. The real data

©CMBI 2008

Quality of Data

SwissProt

• Data is only entered by annotation experts

EMBL, PDB

• Everybody can submit data• No human intervention when submitted;

some automatic checks

©CMBI 2008

SwissProt database

• Database of protein sequences derived from:- translations of DNA (from EMBL Database)- adapted from the PIR collection- extracted from the literature - and directly submitted by researchers

• 385721 entries (may 2008)• Ca. 200 Annotation experts worldwide• Keyword-organised flatfile• Obligatory deposit of in SwissProt before publication

Presently, databases are being merged into UniProt.

©CMBI 2008

SwissProt records

ID identification line

ID ENTRY_NAME DATA_CLASS; MOLECULE_TYPE; SEQUENCE_LENGTH.ID CRAM_CRAAB STANDARD; PRT; 46 AA.

Format for the ENTRY_NAME: NAME_SPECIES ( 12 characters)

For number of organisms (16) recognizable names: HUMAN, MOUSE, CHICK, BOVIN, YEAST, ECOLI….

N.B. The ID can change, e.g. serotonine receptors have got a new nomenclature

©CMBI 2008

SwissProt records

AC accession numberAC P01542;AC is unique:Name, sequence, everything can change but AC stays the same

DT deposition dateDT 21-JUL-1986 (Rel. 01, Created)DT 30-MAY-2000 (Rel. 39, Last sequence update)DT 30-MAY-2000 (Rel. 39, Last annotation update)1) You can not see what the last annotation update was2) No depositor record (Implicit: author of first reference)

©CMBI 2008

SwissProt recordsDE descriptionDE CRAMBIN.DE 6-phosphofructo-2-kinase 1 (EC 2.7.1.105) (Phosphofructokinase 2 I)General descriptive information

GN gene name GN THI2.

OS & OC & OGOS Crambe abyssinica (Abyssinian crambe).OC Eukaryota; Viridiplantae; Embryophyta; Tracheophyta; OC Magnoliophyta; eudicotyledons; Rosidae; Brassicales;OC Brassicaceae; Crambe.Organism Species; Organism Classification; Organelle

©CMBI 2008

SwissProt records

RN ReferencesRN [1]RP SEQUENCE.RX MEDLINE; 82046542.RA Teeter M.M., Mazer J.A., L'Italien J.J.;RT "Primary structure of the plant protein crambin.";RL Biochemistry 20:5437-5443(1981).

CC Comments or notesCC -!- FUNCTION: THE FUNCTION OF THIS HYDROPHOBIC PLANT SEED PROTEINCC IS NOT KNOWN.CC -!- MISCELLANEOUS: TWO ISOFORMS EXISTS (MAJOR ONE SHOWN HERE)CC AND A MINOR FORM SI.CC -!- SIMILARITY: BELONGS TO THE PLANT THIONIN FAMILY.

©CMBI 2008

SwissProt records

DR Database Cross ReferenceDR PIR; A01805; KECX. DR PDB; 1AB1; X-ray; @=1-46. DR PDB; 1CBN; X-ray; @=1-46. (…)DR PDB; 1JXY; X-ray; A=1-46. DR InterPro; IPR001010; Thionin. DR Pfam; PF00321; Thionin; 1. DR PRINTS; PR00287; THIONIN. DR PROSITE; PS00271; THIONIN; 1.

KW KeywordNot standardized (under control of depositor)KW Thionin; 3D-structure.

©CMBI 2008

SwissProt records

FT Feature table data

FT DISULFID 3 40FT DISULFID 4 32FT DISULFID 16 26FT VARIANT 22 22 P -> S (IN ISOFORM SI).FT VARIANT 25 25 L -> I (IN ISOFORM SI).FT STRAND 2 3FT HELIX 7 16FT TURN 17 19FT HELIX 23 30FT TURN 31 31FT STRAND 33 34FT TURN 42 43

©CMBI 2008

Feature table (continued)

Other features: post-translational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. Sequence conflicts between references are also included. FT CONFLICT 33 33 MISSING (IN REF. 2).FT MUTAGEN 123 123 G->R,L,M: DNA BINDING LOST.FT MOD_RES 11 11 PHOSPHORYLATION (BY PKC).FT LIPID 1 1 MYRISTATE.FT CARBOHYD 103 103 GLUCOSYLGALACTOSE.FT METAL 87 87 COPPER (POTENTIAL).FT BINDING 14 14 HEME (COVALENT).FT PROPEP 27 28 ACTIVATION PEPTIDE. FT DOMAIN 22 788 EXTRACELLULAR (POTENTIAL).FT ACT_SITE 193 193 ACCEPTS A PROTON DURING CATALYSIS.

©CMBI 2008

SwissProt records

SQ sequence headerSQ SEQUENCE 46 AA; 4736 MW; 919E68AF159EF722 CRC64;

Sequence data TTCCPSIVAR SNFNVCRLPG TPEALCATYT GCIIIPGATC PGDYAN

Termination line//

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SwissProt entry in MRS

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SwissProt entry in MRS

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SwissProt entry in MRS

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EMBL database

Nucleotide database

– EMBL: 114 million sequence entries comprising 215 billion nucleotides (March 2008)

– Of which EMEST: 50 million sequence entries comprising 27 billion nucleotides (March 2008)

– EMBL records follows roughly same scheme as SwissProt

– Obligatory deposit of sequence in EMBL before publication

– Most EMBL sequences never seen by a human

©CMBI 2008

Protein Data Bank (PDB)

Databank for macromolecular structure data (3-dimensional coordinates). Started ca. 30 years ago (on punched cards!)

Obligatory deposit of coordinates in the PDB before publication

~ 44000 entries (Aug 2007) ( ~2500 “unique” structures)

PDB file is a keyword-organised flat-file (80 column)1) human readable2) every line starts with a keyword (3-6 letters)3) platform independent

©CMBI 2008

PDB records

Filename= accession number= PDB CodeFilename is 4 positions (often 1 digit & 3 letters, e.g. 1CRN)

HEADERdescribes molecule & gives deposition dateHEADER PLANT SEED PROTEIN 30-APR-81 1CRN

CMPNDname of moleculeCOMPND CRAMBIN

SOURCEorganismSOURCE ABYSSINIAN CABBAGE (CRAMBE ABYSSINICA) SEED

©CMBI 2008

PDB recordsAUTHORAUTHOR W.A.HENDRICKSON,M.M.TEETER 1CRN 6

Revision dateREVDAT 5 16-APR-87 1CRND 1 HEADER 1CRND 2REVDAT 4 04-MAR-85 1CRNC 1 REMARK 1CRNC 1REVDAT 3 30-SEP-83 1CRNB 1 REVDAT 1CRNB 1REVDAT 2 03-DEC-81 1CRNA 1 SHEET 1CRNB 2REVDAT 1 28-JUL-81 1CRN 0

REMARK There are very many different REMARK records & subrecords! Not standardized.REMARK 1 REFERENCE 3 1CRNC 10REMARK 1 AUTH M.M.TEETER,W.A.HENDRICKSON 1CRN 16REMARK 1 TITL HIGHLY ORDERED CRYSTALS OF THE PLANT SEED PROTEIN 1CRN 17REMARK 1 TITL 2 CRAMBIN 1CRN 18REMARK 1 REF J.MOL.BIOL. V. 127 219 1979 1CRN 19REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 070 1CRN 20REMARK 2 1CRN 21REMARK 2 RESOLUTION. 1.5 ANGSTROMS. 1CRN 22

©CMBI 2008

PDB records

SEQRESSequence of protein;Be aware: Not always all 3d-coordinates are present for all the amino acids in SEQRES!!SEQRES 1 46 THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE 1CRN 51SEQRES 2 46 ASN VAL CYS ARG LEU PRO GLY THR PRO GLU ALA ILE CYS 1CRN 52SEQRES 3 46 ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR 1CRN 53SEQRES 4 46 CYS PRO GLY ASP TYR ALA ASN 1CRN 54

HET & FORMULHET NAD A 1 44 NAD CO-ENZYME 4MDH 219HET SUL A 2 5 SULFATE 4MDH 220HET NAD B 1 44 NAD CO-ENZYME 4MDH 221HET SUL B 2 5 SULFATE 4MDH 222FORMUL 3 NAD 2(C21 H28 N7 O14 P2) 4MDH 223FORMUL 4 SUL 2(O4 S1) 4MDH 224FORMUL 5 HOH *471(H2 O1) 4MDH 225

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PDB recordsHELIX/SHEET/TURNSecondary structure elements provided by the crystallographer (subjective).HELIX 1 H1 ILE 7 PRO 19 1 3/10 CONFORMATION RES 17,19 SHEET 2 S1 2 CYS 32 ILE 35 -1 TURN 1 T1 PRO 41 TYR 44

SSBONDdisulfide bridgesSSBOND 1 CYS 3 CYS 40 SSBOND 2 CYS 4 CYS 32

CRYST1, ORIG, SCALEcrystallographic parametersCRYST1 40.960 18.650 22.520 90.00 90.77 90.00 P 21 2 1CRN 63SCALE1 .024414 0.000000 -.000328 0.00000 1CRN 67SCALE2 0.000000 .053619 0.000000 0.00000 1CRN 68SCALE3 0.000000 0.000000 .044409 0.00000 1CRN 69

©CMBI 2008

PDB records

ATOMOne line per atom with, unique name and x,y,z coordinatesATOM 1 N THR 1 17.047 14.099 3.625 1.00 13.79 1CRN 70ATOM 2 CA THR 1 16.967 12.784 4.338 1.00 10.80 1CRN 71ATOM 3 C THR 1 15.685 12.755 5.133 1.00 9.19 1CRN 72ATOM 4 O THR 1 15.268 13.825 5.594 1.00 9.85 1CRN 73ATOM 5 CB THR 1 18.170 12.703 5.337 1.00 13.02 1CRN 74ATOM 6 OG1 THR 1 19.334 12.829 4.463 1.00 15.06 1CRN 75ATOM 7 CG2 THR 1 18.150 11.546 6.304 1.00 14.23 1CRN 76ATOM 8 N THR 2 15.115 11.555 5.265 1.00 7.81 1CRN 77ATOM 9 CA THR 2 13.856 11.469 6.066 1.00 8.31 1CRN 78ATOM 10 C THR 2 14.164 10.785 7.379 1.00 5.80 1CRN 79ATOM 11 O THR 2 14.993 9.862 7.443 1.00 6.94 1CRN 80

TER The TER record terminates the amino acid chainATOM 325 OD1 ASN 46 11.982 4.849 15.886 1.00 11.00 1CRN 394ATOM 326 ND2 ASN 46 13.407 3.298 15.015 1.00 10.32 1CRN 395ATOM 327 OXT ASN 46 12.703 4.973 10.746 1.00 7.86 1CRN 396TER 328 ASN 46 1CRN 397

©CMBI 2008

PDB records

HETATMatomic coordinates for atoms within "non-standard" groups (cofactors, ions, …) and for water molecules

HETATM 5158 AP NAD B 1 42.641 30.361 41.284 1.00 26.73 4MDH5495HETATM 5159 AO1 NAD B 1 43.440 31.570 40.868 1.00 20.69 4MDH5496HETATM 5160 AO2 NAD B 1 41.161 30.484 41.376 1.00 33.73 4MDH5497

HETATM 5207 O HOH 0 15.379 1.907 3.295 1.00 58.12 4MDH5544HETATM 5208 O HOH 1 58.861 0.984 17.024 1.00 37.58 4MDH5545HETATM 5209 O HOH 2 24.384 1.184 74.398 1.00 35.92 4MDH5546

CONECTconnection records (not obligatory) indicate which atoms are connected (mainly for HETATM)